I checked Coffee.exe and Sonar.exe with
the virustotal website . It failed to find any antivirus programs (it checked over 50) that had any problem with them. It seems therefore unlikely that antivirus programs are causing the disappearances mentioned.
My reason for checking as above was that I had the problem of a well-respected non-CoffeeCup program disappearing. The CEO of the software company checked using virustotal, and was able thus
(a) to identify the antivirus program causing the problem, and
(b) to liaise with the antivirus company to get the false-positive finding and quarantining remedied.
If cleanup programs and malware prove not to be the cause of the problem, and if a solid-state drive is being used, it could be failing. I had an early model fail, causing various troubles in Windows, and it took me ages to find the real culprit. If a traditional rotating hard drive is being used, it might be worth checking for bad sectors or cross-linked files.
Frank