While searching for free/open-source MySQL incremental backups solutions I have found a number of ways to do incremental backups and all of them seem to either rely on "logical" way of backups/restore like mysqldump and binlog (or LSN) or "physical" way (like Percona's xtrabackup). However, in both cases the only scenario implied is backing up the database globally (all databases).
I am looking for the way to provide incremental backups per database: there are two db servers (master and slave) and each handles lots of databases. Each of these databases belong, let's say, to different customers and some of them tend to grow really big. While software upgrades database schema sometimes changes and before the upgrade we must make sure we are on the safe side so backup is a must but full backup is definitely not a way to go due to database sizes.
Please advise how this can be solved or at least suggest some ways to look for solution.