Answer by tk421 for Fast way to get checksum for all files within a huge nested directory

You could look at File integrity monitoring software.

Basically these are designed to detect the introduction of rootkits to filesystems but at the core they have a database for files with meta information (checksum, hashes) and monitor files that have been changed or added under a set of directories which is what you want.

The oldest one I've heard about is Tripwire but an open source version was created called AIDE. A more recent one is OSSEC recommended from https://serverfault.com/questions/141800/recommend-alternative-to-tripwire.