Debian :: File Integrity For Backups Of Home Data ?

I'm currently backupping our home data (pictures, videos, our CDs ripped to FLAC which I spent a lot of time to tag accurately ), totalling almost 300 Gb, on 2 external USB drives, one of which is meant to stay at a friend's. I left the factory msdos filesystem as it was, thinking it could be useful to be able to connect the drives to a windows machine with no problems. It's certainly useful to have «normal» data that I can take with me e.g. when visiting my family.

I'm simply using rsync manually, checking for suspicious changed or deleted file before commiting the change. I do that every 2 weeks or so.

Now I want to add a file integrity management to my backupping scheme: I want to be able to check that new data I'll be committing has not been tampered with (integrity check before updating tags on my main drive), and I want to be able to check that backupped data is still sane on my USB drives, especially if I need to recover from data corruption on my main drive.

Since I'm essentially mirroring the data, I thought run of the mill integrity software would let me just rsync the integrity database, and I'm done.

But after browsing through the docs of tripware, afick and the like, I fear they work only with absolute paths, so the database for my main drive wouldn't work for my USB drive, that's mounted elsewhere when I plug it in, obviously.

So, I feel I'm missing something. It looks to me I'm trying to solve a very common problem, how do people do it?

Did I miss a file integrity software that works with backups?

Is there a trick like using a symbolic link pointing to whatever file hierarchy I want to check, and have tripware/afick/... monitor that link?

Should I run a more elaborate backupping system than plain rsync? Which one? (Storebackup for instance looks promising since it involves md5 sums, but it's targetting a completely different problem, and I'm not sure I can use it at all for what I need.)