[tsac]

Details would help with your problem.

Some issues.
A while ago Yahoo had issues with their sync of users contacts and essentially deleted them from the users PC or cell phone.
If you are using Link to sync you need to check the direction of the sync, to cell or from cell or both.
Depending on how , if using Outlook you can wipe out contacts if you select the wrong contact list ( I have done this) and it will replace the one on the phone.

Memory issues. 1000 contacts seem like a lot and you need to check available memory.

BBM contacts replaced the others. the two lists are separate so it is possible you replaced the other.

If you have more details on how you sync and what you use to sync contacts like PC or OTA using a server it will help anyone who may have more ideas.