We had this issue in the past and believed it was caused by BIDS deploying a solution with unsufficient permissions, but last weekend, we had this issue where we are 100% sure nobody used BIDS.
What happened: for several (7 out of 15) databases all content disappeared (cubes, dimensions, datasources, etc), but the DB folderstructure remained in SSAS.
Only solution: restore from backup.
I'm using SQL2008R2 SP1.
Any help more than welcome
Geert Vanhove