Why do my user preferences get lost on reboot?

Apple Mail, the OS bluetooth subsystem and some other applications (e.g. Fantastical and Things app) loose relevant (but not all) configuration and preferences on nearly every reboot. For Apple Mail it seems that all lost settings are stored in the file ~/Library/Containers/com.apple.mail/Data/Library/Preferences/com.apple.mail.plist. I haven't yet identified the other affected files. It does not happen if I hunt for it (keep rebooting), but only after using the Mac for a while. I currently run macOS 10.15.6 on a MacBook Pro 16" with only a few popular Apps from the App Store plus Microsoft Office. I am a long term Mac user. The bad behavior started approximately 2 years ago after an update to macOS High Sierra (I think). The Mac became more a more unusable because of this and other strange bugs (it also started to become extremely slow, so I had to reboot regularly, loosing all settings afterwards). Repairing and even installing the OS did not help. Therefore, I got a new Mac and installed everything from scratch (no restore from a backup) and installed only very little software on the system. However, the preferences still get lost on nearly every reboot! What could cause the file contents to be lost on nearly every reboot?