You may want to check out the repair command. It seems to show that TMSU keeps track of file locations on disk. If you move a file, it can find it if it hasn't been modified. If you move and modify a file, it can't find it and will mark it missing.
They stick better with files, as long as your tools know about them and handle them fine. Weakness is that they can (will) get lost in tools that do not. There are many of them: zip-unzip, tar-untar, http requests, ftp, etc.
https://github.com/oniony/TMSU/blob/master/src/tmsu/cli/repa...