That sounds like a lot of work to do when you think about it.

You should either add a Client ID to each table to preserve uniqueness when merging all the databases. You must add this to your code every time you call one of these tables.

Another option would be to add a prefix (to char based keys) or a base number (to int keys). But this will change all of your keys and have to review the code.

You won't find an easy option for this project and it might take you a while to test everything.

An option would be to automize the administration. It won't fix the problem but it will give you more time to implement the changes.