Recently we used mergecontendbs and lost some data during the merge. The issue was,
Stsadm -o mergecontentdbs operation does not copy
dbo.AllUserDataJunctions table to the new database, while deleting it from the source database. This results in major dataloss every multi value lookup column will lose its value.
We found this is a bug if you are on MOSS service pack 2. So please install April CU 2009 that was release after SP2 before you do the merge content dbs.