No. Your game code is a new class, in whats called a module, which is fully supported by the engine. Your game code almost definetly relies on the same stable APIs that a GDExtension or GDScript itself uses. There will be no merge conflicts, no problems, almost certainly.

Note: We have a fork of godot that has some changes and fixes weve made and engine upgrades are still a breeze. Solving the odd merge conflict is not that hard, people do it all the time. Godot's code base isnt drastically changing from day to day. 3->4 only had significant impact if you were doing certain things with the 'visual server'... other than that even that was easy.