Whenever I change and overwrite Mod Vehicle Configs, they are reset every Game Start. For Example: FAIT One Hungary Police Skin + Config has missing Wheels. When I change the Config so it has Wheels again, save and overwrite the old Config, as soon as the Game Restarts it has no wheels again. Same for the Schoolbus, where I changed the Stock Congfig to a different Engine, as soon as the Game Restarts it's back to the old engine. I disabled "Automatic Mod Updates" but that doesn't solve the Problem.
When you save a config through the parts selector it saves it at Documents/BeamNG/Vehicles/vehiclename/configname.pc But the ingame configs are in the program files/beamng/content/vehicles/vehiclename.zip/vehicles/vehiclename/configname.pc Making a new config with the same name as an old config means that the game sees 2 conflicting files. It used to be that it favored the usermade files, if there are duplicates. (IIRC) Now, however, it favors the in-game file. But they didn't change the config save and load menu to clarify that. I would just recommend using a different config name.
You can have fancy configs with pics despite this. If you place a info_configname.json and a configname.jpg in the same folder as the actual config that should work. I would recommend just looking at other info_configname.json's to see what they look like and what's in there. There used to be a feature in the game that calculated the vehicle specs, but that has been broken for a while. (TBH I don't even know if you need the .json file. I'd just start with placing a .jpg with the same name in the same folder and seeing what happens)
That's not meant, but a bug. The game is meant to still give priority to the files in userfolder. We found the issue already fixed in for the next update too.