Vista - Vista offline sync deleted users offline files. Any suggestions?

Our My documents redirect server was setup improperly. The folder
structure was chaotic and the permissions were all over the place.
Some folders were viewable by any one and some were locked down so
tight I couldn't back them up properly.

I took the server offline, cleaned up the folder paths and
permissions. Modified the gpo's to point to the updated paths. It
was the same server, just different path. That is the only thing I
changed in the GPO.

We have several Vista users that worked offline during this time.
When the server came back online their offline changes were deleted.
This happened to several (maybe all) Vista users who modified files
while offline.

So,does anyone have any advice on correcting this? I just can't see
why it would delete these files. That is just downright dangerous.

-a little frustrated. Just had to tell 2 users they lost a weeks
worth of work.