Merging multiple SMS databases
I believe /data/data/com.android.providers.telephony/databases/mmssms.db is an SQLite DB, so you can use this firefox add-on, SQLite Manager and that should let you merge whatever backups you have lying around rather easily. 

After you merge them, you can just replace /data/data/com.android.providers.telephony/databases/mmssms.db with the resultant merged file (backup the oringal first).