File Corrupted Error

Hello there. Some of you may have seen this error before. "File corrupted!. This program has been manipulated and maybe it's infected by a virus or cracked. This file wont work anymore.". I am wondering which library/dll is prompting this message. In my case it occurs if I edit a specific exe(even a single bit) without actually breaking it.
Why are you changing a bit in an exe file? Not sure but maybe the exe format has some kind of checksum and if you change the file the checksum will no longer be correct.
I'm trying to get rid of a function call alongside with the parameters being pushed by nop'ing them. Looks like either I have to somehow modify MapFileAndCheckSum before it's being called or nop the address during runtime.
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