How would you lose them when you recompile? Updating and rebuilding the source doesn't affect your database at all, unless they did an update regarding a new column in a table. However, not sure where you get "I'll lose my database when I update and rebuild the source.."
Honestly, don't even bother updating with TrinityCore every time they do an update, it isn't recommended at all. Why? They don't test their changes before committing which results in potential server crashes and issues with the source until they fix it. I don't even recommended running their SQL updates because if you see that malcrom guy add new SQL updates, he does at least 4 commits before fixing syntax errors, typos, etc (That goes for some other people too)..
What I recommend doing is cherry pick each IMPORTANT and STABLE updates, most likely done by pull requests and not from the actual TC team.
To sum it up, you won't lose anything when recompiling after you updated your source. If you updated anything via C++, it can sometimes conflict with a TC update, but it won't overwrite it.