When I restore files from a backup I've cp to my /home it creates a symbolic link to backup of vmlnuz-3....etc and initrd.img.. When I boot it refers here for the files and not the boot/vmlinuz etc... That is when it boots it looks in boot but the vmlinuz etc files are symbolically linked to the backup and I get a /sbin/init ..Permission denied. I can see that it has just done a symbolic link when viewed in list view in
caja.

How can I force it to ACTUALLY copy files to the boot directory and stop just creating a symbolic link to the backup files instead? Then I may be able to boot the ACTUALLY restored backup.

Sorry but this has caused me many lost hours before I realised what it had done.

Then the first question is: how do you make backups? Because usually you would use something like 'rsync' or some front-end or a backup application? The reason for asking is if you used rsync then you would do a reverse rsync by switching the source and target directory, possibly with using --dry-run before committing, and if you use some backup application then it should guide you in restoring files. Personally I'd use the command line for such critical tasks instead of some GUI. While dragging and dropping files may seem convenient at first the command line allows you full control and doesn't inadvertedly create symbolic links as file managers may think you want to.