Hey,
Now it seems GC3 does some sort of file integrity check and my modified EXP1_MercenaryDefs.xml file is rejected.
Are you saying that the game rejected a EXP1_MercenaryDefs put in the mod folder?
To clarify, I've been working on a mod for awhile now and wanted to remove the United Earth faction from the game, so I put a copy of DLC6_FactionDefs in the Documents/GalCiv3/Mod/Game folder, and replaced the contents with a junk string table. Since then I haven't had the UE in game nor any problems, from that file at least
Placing a file with the exact name as the original, and in the right folder (e.g. mod/game) should overwrite the original without the game counting it as a broken file. If this isnt working, I suggest contacting SD's technical support. This thread explains the basics in detail https://forums.galciv3.com/473442
Hope this helps and sry if this is just a post about what you already know.