If i may ask, why do you still use binary files for the server? and not actual source code file releases? You are simply ending up very limited in terms of what you can change/edit fix by working with old binary files. I know most devs here did that around 10 years ago, but lots has changed since then and tools and software and releases has exploded the last few years with good and stable source releases
Most of the problems you are experiencing are extremely old legacy issues that in most cases normal binary files have fixed as a "temporary" solution, while in source its fixed for good so it can never ever happen anymore. Isnt it better to have full freedom of the files you work on with using the source code? and especially now with AI too! Anything you want can be implemented as long as you have an active AI subscription! (and that goes for any Bugs fixed too!)