Use it at your own risk! You might end up worse than before. Backup everything beforehand. Twice.
If you have the Messages app setup in multiple Macs with the same Apple ID you may end up with iMessages (or SMS) scattered around all of these Macs. This is because after a certain time the new iMessages (or SMS) recevied will cease to push to devices afer a certain time has elapsed. Thus, if a computer has been offline for some period of time it won't get the new iMessages.
Each Messages instance stores the information in a SQLite database, to consolidate all these databases run the script below. This is where the Messages app stores the SQLite database under ~/Library/Messages, the folder contents will look like as follows:
- chat.db