I have a FIMS system that tells me that DLLs/EXEs have changed. If those are Windows DLLs and we just did Windows update, I can assume they are not corrupted, but how do I know for sure?

Is there a location where I can get the correct checksum for a given Windows DLL / EXE?

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You can run the System File Checker by using the command sfc /scannow /verifyonly (verifyonly is only availabale in 2008+). See Description of the Windows File Protection feature for more details. Microsoft does have a File Checksum Integrity Verifier utility however I am unaware of any "default" list of checksums as that list would change depending on which hotfixes were applied, drivers, etc. (thus the creation of the SFC)

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