I am having an issue with the Microsoft Malware Removal Tool version October 2018 detecting RU Host 6.9.4 files as threats and deleting them. Just thought I'd share in case anyone else was having this issue or plans to use MRT.exe on clients PC's. Luckily I use two different remote programs so I was able to reinstall RU through my other program and then re-ran MRT.exe to verify that it was in fact the source of the problem.
Unfortunately, we couldn't reproduce the issue. Just downloaded and ran Microsoft MRT on a Windows 10 machine with all Remote Utilities modules installed, including RU Server , but neither was deleted or marked as infected. They are working normally.
Here is the scan result:
Perhaps, the removal tool signature base was updated since the time you ran it?