We have a 1TB storage server I've just gone to transfer a 100Gb file across to it. And it has deleted the shadow copy. From Googling I understand that this probably occurred: http://support.microsoft.com/kb/826936
Is there any way of recovering those shadow copies back?
Thank you very much for having a read anyhow and any help would be greatly appreciated.
Assuming you stored your volume shadow copies on the same disk that you just moved the 100GB file onto you're probably out of luck. Undelete on NTFS, especially after making changes to the volume, is iffy at best.
Shadow copies aren't backup. They're a nice crutch to help you recover files in some situations, but they shouldn't be relied upon as existing for any allotted time since they can be pruned by the OS automatically for space reasons, or due to unintended behaviors (as you've seen).
Shadow copies will get created on your normal schedule. So long as the original files are still present why worry about the loss of a specific shadow copy?
Also shadow copies are just one way to have alternate revisions and are a convenient way to "undelete" files. They are not however a backup. You need to be backing up to LTO or to disks on another server on a regular basis so that if the drives where the original data lies and the drives where the shadow copies lie (possibly on the same physical disks, and likely in the same physical enclosure) fail or are destroyed you can restore from/to different equipment and media.
Keep using shadow copies but for performance/reliability reasons don't store those copies on the same physical disk if you can avoid doing so. Absolutely never on the same partition even if it is on the same physical disk (it will cause severe fragmentation all the time and increase the IO load part of the time).