I'm glad to hear that it's useful to you!
There's no reason that updating should mess with the settings. Have you tried the latest alpha? I did find a problem recently that could cause problems with the updater closing the application where settings could in some cases be lost. But the new alpha of CHS should solve that problem.
2. Interesting idea, will consider.
3. Difficult because the location of database and configuration options are governed by that option and so it needs to have a way for you to specify that BEFORE it loads the options file.
4. Noted, will be fixed in new release.
5. Maybe I can make an option that says to clear settings on opening modify format dialog.
6. I will implement that after I implement a cure to covid.