As @drachenfeles said.
The configuration of the tool is stored in the INI files of the game server, there’s no other configuration files to mess up with so if you have 1.0.46 running and want to update, you don’t even have to shut down your server:
- download the new executable and put it where the previous 1.0.46 was (don’t even have to remove 1.0.46, so you can easily go back to the previous version if you found a problem).
- close 1.0.46
- start 1.0.47
Normally the tool will detect that the server is running and continue from where it was, without any disruption on restart times or update checks.
Let say that the team has been doing some late work these few last days.
The main problems the team had, was that there was a few miss-reported errors which led to search for problems where they were not, which kind of delayed things (like some of the reported FLS errors were not FLS errors at all but Steam errors caused by the start of the Sumer Sales), but there’s now a proper list of issues, and the team is going through them and trying to do regularly hot-fixes to fix things one at a time.
Generally speaking, the better the reports, the more chances the issues get fixed 
Useless report:
My server is crashing! Plize fix! Now!
Usable report:
My Server XYZ, hosted on QWE is crashing on startup, I’ve tried with and without mods, same issue, I noticed there was many “Warning: Blablabla” and “Error: Bliblib lib” which were not present in the previous versions, here are the log files and a crashdump of the server when it happened.