On my Import settings (for each import folder), I uncheck the "Ignore files previously removed from library" - I *think* this causes MC to not add files to that Removed database - mine is always empty after MC restarts.
That is correct.
Actually no. MC still adds files removed from the Library to the Removed Database. It is just that you two have "Ignore files previously removed from library" set so MC re-imports any files you delete next time Auto Import runs, if those files still exist, and the files are removed from the Removed Database when they are re-imported.
If you have "Fix broken links" in Auto Import set to "No", then files that no longer exist will remain listed in MC. When you delete those missing files from the Library they will be added to the Removed Database, but when Auto Import runs with or without "Ignore files previously removed from library" set they will be removed from the Removed Database, and of course, aren't imported back into the Library.
We seem to have covered stuff that was discussed before, but that is okay. It is reinforcing the issues with some settings.
1. Auto Import turned off so it doesn't automatically run in the background, but only when manually run, stops MC scanning for new files regularly.
2. Turning off "Display missing file image in lists (slow on network drives)" and don't use IsMissing() anywhere it is always displayed (Status Bar), or unnecessarily in Views, without understanding the consequences.
3. Decide how to manage files removed from the Library when they aren't removed from disk. Be aware of the consequences of "Ignore files previously removed from library", particularly in combination with "Fix Broken Links" settings.
4. When restoring Library Backups from earlier versions, restore Settings as well, if you want MC to behave in the same way as the earlier version. But also check the MC Options to be sure all settings are as you wish. Sometimes with functional changes in later versions, MC will set some Options back to defaults, so that no invalid Options are left in place, or for perceived performance or usability of MC.