Panic over everyone.

I run an ls -a on the folders and found the cause of the problem, the files were hidden with a "._" prefix making them hidden.

Removed all those and the system returned to normal.

Thanks all.

@herb_fargus Its an idea but I do not have any spare usb drives.

Thank you for that super-fast reply! I was looking at gparted but hadn't managed to get onto it around work - but that auto script seems to be just the ticket! I'll give it a crack and come back if something goes horribly wrong - if it doesn't we can assume this thread is closed :D

@edmaul69 Worked. Thank you.