Installation messed up security settings for my Program Files folders

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I just activated my license and am already seriously regretting installing this product. The first thing this product did was detect a program that I know for a fact is not a virus and deleted the executable file. Didn't quarantine it, didn't move it to recycling bin, just flat out hard deleted the file without any confirmation whatsoever. Now I add the folder to the 'do not scan' list, and try to redownload the program and move the executable file back to where it was. Except now my Program Files folders have their security settings completely 100% screwed up and I cannot get access to it back. I am now locked out of modifying anything in my Program Files folders, despite trying to set security settings back to the way they should be. But it seems to be irreversibly damaged. Has this happened to anyone else? How do I get access to these folders back?