Unity 4.0, Exchange2000. I used the Bulk Edit utility to add some Alternate Extensions to about 14 users. After it was done, I went in to look at them, and there were no Alternate Extensions listed. Previous Alternate Extensions that I had in there were gone as well. Is this a known bug with the tool. I did make sure that the "remove all alternate extensions for selected subscribers" checkbox was unchecked.
Nancy just made an observation that may be what you're seeing here - this same type of thing (though not exactly as you describe it) was reported as a problem in CUBI with alternate extensions. There were two different looking bugs filed for this that turned out to have the same root cause:
Short story is the synchronization service that writes updated information from SQL to AD was choking and not getting alternate extensions properly - which had the effect of wiping them out in some cases. This could be what you're seeing - I'm testing on 4.0(2) and my 4.0(3.81) boxes (4.0(4) pre release) and don't see this issue - this bug was specific to 4.0(3) release.
This is fixed in 4.0(4) (not released yet) - I'm checking to see if it was bundled into an ES or not.