Script Editor "Script file has changed externally, do you wish to update"

This is an infuriating one for sure. I've found a condition where any time you try to remove lines from code and recompile, and the compilation fails, it refuses to let you remove those lines of code, continuing to have the dialogue pop up until you click yes, where it reverts back to the code you wanted to delete. Never had this issue before but it's driving me nuts.