DLP Best Practices for Temporary Files

hello after running discover scans we have found thousands of events and matches with confidential data stores in temporary files such as appdata\local and iecache. I wanted to know what is the best practice for getting these directories cleaned up with out resetting any default settings for applications that maybe set. There is concerns that if we delete those temp files it will reset the default settings for other applications that may be using those files in there.