OK this is what I did to solve the problem.
I made a Clone of the VM then did the following.
1. I used fdisk to change /dev/sda2 from lvm to Linux
3. Shut down the VM and booted into Gparted
4. I deactivated sda2 and increased the size by all available space (Still showed as lvm at this stage)
5. I reactivated sda2 and shutdown Gparted.
6. I booted into the VM
7 fdisk shows the following:
Disk /dev/sda: 42.9 GB, 42949672960 bytes
255 heads, 63 sectors/track, 5221 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x0002b93c
Device Boot Start End Blocks Id System
/dev/sda1 * 1 64 512000 83 Linux
Partition 1 does not end on cylinder boundary.
/dev/sda2 64 5222 41430016 83 Linux
Everything looks OK and I can open the web server and see the files....
I think that the problem is fixed, and I take no responsibility if you try and it fails to work
EDIT: This did not fix the problem just looked like it did. I deleted it all and started again