We have recently migrated to ESXi 4.0 from ESX 3.5, and the upgrade went smoothly. We decided to adopt vDR as initial testing has been positive, it has been backing up several of our VM's without any problems, until last night when I set it to backup only the C: drive and H: drive VMDK's of a multi-disk server, it seems to have gotten itself confused and in the process has deleted the unticked "data" disks completely - without trace.

Our VM (called "fs1") has 5 disks which were allocated accordingly (each disk in it's own datastore+LUN on the SAN)...

C: 20GB (vmstore1/fs1.vmdk) OK
E: = 450GB (filestore1/fs1file1.vmdk) deleted!
F: = 500GB (libstore1/fs1lib1.vmdk) deleted!
G: = 500GB (libstore2/fs1lib2.vmdk) deleted!
H: = 500GB (libstore3/fs1.vmdk) OK

As you can see, the two that are named the same were untouched, but the 3 that were not ticked got wiped out!

I went onto the "unsupported" console to verify with my own eyes as the datastore browser can give varying results... none of the extra disks from this particular VM were there... the folder structure was there, but the vmdk and -flat files were missing.
I know this sounds crazy, but it's the only coincidental thing I can find that may have been the cause - that and the two disks happen to be named the same (which is why they were both ticked in the vdr Backup screen as it wasn't obvious which disk was which).

I've yet to create a support ticket as I'm busy recreating the data stores and doing a restore. If I get chance I'll try to recreate this in a dev lab, or if someone else could I would be greatful.

Edit just to say, the only errors that appeared in the events was this by the vDR backup user around the time the VM went offline (due to losing its disks), an error -3941 failed to create snapshot:

"Create virtual machine snapshot
fs1
File <unspecified filename> is larger than the maximum size
supported by datastore '<unspecified datastore>"