I am running 2 rsync commands , one after the other.

The first does a rsync over ssh to sync between a owncloud server and a backup server:

rsync -v -a -H -i -L -e ssh --delete --link-dest=/mnt/backup01/sun/var_www_owncloud/sun_oc_9999999999_current user@domain.org:/var/www/owncloud /mnt/backup01/sun/var_www_owncloud/sun_oc_1501355550_F_Sat_29Jul2017_2012

I then user rsync again to sync between the main backup drive /mnt/backup01/ and the second backup /mnt/backup02/

rsync -aviH --delete /mnt/backup01/ /mnt/backup02/

Thing is when the first one changes verry little

07/29/17_20:12 backup(8517) receiving incremental file list
07/29/17_20:12 backup(8517) created directory /mnt/backup01/sun/var_www_owncloud/sun_oc_1501355550_F_Sat_29Jul2017_2012
07/29/17_20:12 backup(8517) cd..t...... owncloud/database_backup/
07/29/17_20:12 backup(8517) >f+++++++++ owncloud/database_backup/owncloud-sqlbkp_20170729_1955.sql.gz
07/29/17_20:12 backup(8517) >f+++++++++ owncloud/database_backup/owncloud-sqlbkp_20170729_2010.sql.gz
07/29/17_20:12 backup(8517)
07/29/17_20:12 backup(8517) sent 11,815 bytes received 20,381,648 bytes 1,235,967.45 bytes/sec
07/29/17_20:12 backup(8517) total size is 412,002,742,657 speedup is 20,202.69
/mnt/backup01/sun/var_www_owncloud/sun_oc_9999999999_current
07/29/17_20:12 backup(8517)

The second is deleting everything and then adding it back.

Any idea how to fix this?

What file system is /mnt/backup02/ using? If it's something like NTFS, you'll need to introduce a "modify-window" because it can't save date-time with the precision of ext4 or other *nix file systems.

So, you'd change from this:
to this:
Honestly, I don't know exactly what iH flags do. My usual thing if doing a backup to NTFS is this:

These flags are:
-t preserve modification times
-v verbose feedback
-l copy links as symlinks
-r recursive (going through the full directory tree)
--delete delete files that don't exist in the source
--modify-window=5 consider date-time within 5 seconds to be good enough (to compensate for NTFS limitations)

Note that the only file attributes this attempts to replicate are modification times and saving links as symlinks. I think that if the target file system is NTFS, it's more trouble than it's worth to attempt to replicate more than that.

both ext4 (conecxted with usb3).

-H is preserve hard links
-i gives info (thats why I havew '>f+++++++++' above)

Then my guess is that it has something to do with hardlinks, but I'm not familiar with using them and rsync to know what could be going on. I only use symlinks.

Does the "-i" output for that second run not give any clues about what is going on? You've shown the output for just the first (successful) run, which isn't very helpful. Just the output related to one or two of the affected files is sufficient.

...
07/30/17_04:05 mirror_drives(10108) rsync -aviH --delete /mnt/backup01/ /mnt/backup02/
07/30/17_04:05 mirror_drives(10108) sending incremental file list
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/Pipes/WindowsPipes.php
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/Pipes/UnixPipes.php
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/Pipes/PipesInterface.php
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/Pipes/AbstractPipes.php
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/Pipes/
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/Exception/RuntimeException.php
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/Exception/ProcessTimedOutException.php
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/Exception/ProcessFailedException.php
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/Exception/LogicException.php
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/Exception/InvalidArgumentException.php
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/Exception/ExceptionInterface.php
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/Exception/
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/phpunit.xml.dist
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/composer.json
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/README.md
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501345801_H_Sat_29Jul2017_1730/owncloud/updater/vendor/symfony/process/ProcessUtils.php
0
...
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501174201_H_Thu_27Jul2017_1750/owncloud/.user.ini
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501174201_H_Thu_27Jul2017_1750/owncloud/.htaccess
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501174201_H_Thu_27Jul2017_1750/owncloud/
07/30/17_04:05 mirror_drives(10108) *deleting sun/var_www_owncloud/sun_oc_1501174201_H_Thu_27Jul2017_1750/
07/30/17_04:05 mirror_drives(10108) .d..t...... sun/var_www_owncloud/
07/30/17_04:05 mirror_drives(10108) cLc.t...... sun/var_www_owncloud/sun_oc_9999999999_current -> /mnt/backup01/sun/var_www_owncloud/sun_oc_1501383908_F_Sun_30Jul2017_0405
07/30/17_04:05 mirror_drives(10108) cd+++++++++ sun/var_www_owncloud/sun_oc_1501345801_D_Sat_29Jul2017_1730/
07/30/17_04:05 mirror_drives(10108) cd+++++++++ sun/var_www_owncloud/sun_oc_1501345801_D_Sat_29Jul2017_1730/owncloud/
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501345801_D_Sat_29Jul2017_1730/owncloud/.htaccess => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/owncloud/.htaccess
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501345801_D_Sat_29Jul2017_1730/owncloud/.user.ini => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/owncloud/.user.ini
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501345801_D_Sat_29Jul2017_1730/owncloud/AUTHORS => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/owncloud/AUTHORS
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501345801_D_Sat_29Jul2017_1730/owncloud/COPYING-AGPL => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/owncloud/COPYING-AGPL
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501345801_D_Sat_29Jul2017_1730/owncloud/console.php => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/owncloud/console.php
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501345801_D_Sat_29Jul2017_1730/owncloud/cron.php => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/owncloud/cron.php
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501345801_D_Sat_29Jul2017_1730/owncloud/db_structure.xml => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/owncloud/db_structure.xml
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501345801_D_Sat_29Jul2017_1730/owncloud/index.html => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/owncloud/index.html
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501345801_D_Sat_29Jul2017_1730/owncloud/index.php => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/owncloud/index.php
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501345801_D_Sat_29Jul2017_1730/owncloud/occ => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/ownclo
...
07/30/17_04:05 mirror_drives(10108) cd+++++++++ sun/var_www_owncloud/sun_oc_1501383908_F_Sun_30Jul2017_0405/owncloud/updater/vendor/symfony/process/Pipes/
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501383908_F_Sun_30Jul2017_0405/owncloud/updater/vendor/symfony/process/Pipes/AbstractPipes.php => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/owncloud/updater/vendor/symfony/process/Pipes/AbstractPipes.php
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501383908_F_Sun_30Jul2017_0405/owncloud/updater/vendor/symfony/process/Pipes/PipesInterface.php => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/owncloud/updater/vendor/symfony/process/Pipes/PipesInterface.php
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501383908_F_Sun_30Jul2017_0405/owncloud/updater/vendor/symfony/process/Pipes/UnixPipes.php => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/owncloud/updater/vendor/symfony/process/Pipes/UnixPipes.php
07/30/17_04:05 mirror_drives(10108) hf+++++++++ sun/var_www_owncloud/sun_oc_1501383908_F_Sun_30Jul2017_0405/owncloud/updater/vendor/symfony/process/Pipes/WindowsPipes.php => sun/var_www_owncloud/sun_oc_1501177501_H_Thu_27Jul2017_1845/owncloud/updater/vendor/symfony/process/Pipes/WindowsPipes.php
07/30/17_04:05 mirror_drives(10108)
07/30/17_04:05 mirror_drives(10108) sent 225,125,102 bytes received 49,724,774 bytes 216,673.14 bytes/sec
07/30/17_04:05 mirror_drives(10108) total size is 13,606,976,610,805 speedup is 49,506.94

Ben

It may be to do with this (output from mount)

/dev/sdb1 on /mnt/backup01 type ext4 (rw,relatime,stripe=8191,data=ordered)
/dev/sdc1 on /mnt/backup02 type ext4 (rw,relatime,data=ordered)

Ben

The files being sent are not in the same directory as the ones being deleted. It appears that a new directory "sun/var_www_owncloud/sun_oc_1501345801_D_Sat_29Jul2017_1730/owncloud/" is being created at the destination and then multiple hard links are created in that directory. The files themselves are not being transferred -- the hard links are to existing files in other directories. The same then happens for directory "sun/var_www_owncloud/sun_oc_1501383908_F_Sun_30Jul2017_0405/owncloud/updater/vendor/symfony/process/Pipes/".

None of that is in the directory tree "sun/var_www_owncloud/sun_oc_1501174201_H_Thu_27Jul2017_1750/" that is being deleted.

Thanks, ive gpot to the bottom of it. My rsync comand was not quite right (I had ot add /. to the source. also the devices for the drives swaped when I rebootid, I am now using UUID.