I occasionally had this problem occur in my 3.1(5) Unity server where the information for the subscriber in SA would lose the extension. The information would still be in the UnityDb, so I would scan for the subscriber in SQL and delete the value in the dtmfaccessid field. Then I could re-enter and save via the SA. I have not had a reoccurrence since upgrading to 4.0(3). My first thought is to check replication between your Unity server and AD, for example, is your Unity server registry pointing to a correct global catalog server in your own domain? When we first installed 3.1(5), Unity was pointing to the wrong GC server in another domain in our AD forest and we were having problems getting subscriber information to "stick". TAC was instrumental is helping us identify the problem. To check in the registry, go to HKLM\Software\Active Voice\Directory Connectors\DirSynchGlobalCatalog\1.00\Directory - field DefaultGlobalCatalogServer. The DefaultDomain field is registry path HKLM\Software\Active Voice\Directory Connectors\DirSynchAD\1.00\Directory. Also, are you getting any application event log errors when the subscriber loses the extension information?
Prior to 4.0(3) the DTMF Access ID (extension) was storaged in multiple places in the Unity database. We would update the value in all the different places using SQL triggers but race conditions existed which would cause it to get deleted. So, to correct this we consolidated the DTMF Access IDs to a single table called DtmfAccessId and now use SQL views to associate the value in all the places we need it to be.
Since 4.0(3) I have seen no reports of it vanishing so I think it's corrected. My recommendation is to upgrade to 4.0(3).
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