MacOS launches the wrong binary when clicking on .app

I developed a MacOS application that contains several binaries inside myapp.app/Contents/MacOS
I noticed that after a crash of my application, MacOS sometimes doesn't launch the correct binary. Even if the Info.plist is correctly pointing to the good one.
I found a trick to fix this, it is to move the Info.app to a different directory (let's say myapp.app/) and then move it back (myapp.app/Contents/).
It seems to me that this is a fallback of MacOS after detecting that an error occurred. I would like to understand this process and know how to force the execution of the correct binary or reset whatever cache MacOS keeps.
Any help will be greatly appreciated.

Thanks for your answer. Here are my comments.
I made sure that the problem doesn't come from me (no log in the mainApp, the setting has been correctly updated on disk, the setup is launched as "setup -psnXXXXXX" which means it is the binary started by the OS). Also, it did happen that clicking on the .app launched the other binary (Configuration) at startup which is impossible from my code.
I know where the crash is and I already fixed it. However some of my users are experiencing this behavior after other random crashes. I am working on fixing them all but in the meantime, there must be a way to avoid this buggy behavior.
Thanks again for your help trying to understand this.

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