Best thing you can do is restore the backup to a new database, and then run queries (which will depend on the application(s) using the tables) to identify the rows you want and transfer this data across.
Remember to keep taking backups as you go through this process to limit possible data loss, and make sure the backups aren't overwriting each other as you go.
pt-table-sync could well be of help to you, but you'll need to read up on it thoroughly, specifically the parts about Bi-directional syncing. I haven't used it except to sync master/slave but from what I can see it could well work in your situation (if you restore your backup to another database).
Just remember, take backups before you do any step. Even the restore of the backup to another name. Nothing is going to ruin your day faster than restoring over the top of your current DB.