So regarding the other problem with two installations listed under “Apps and Features”: This is indeed a known issue. Will not happen again with future versions.
We had to change the unique identifier of the installation. We could have done it sooner or later, but decided to no longer defer it as the number of affected users will only increase over time.
That said, the deinstallation should (in theory 
) not have deleted your app settings.
Edit: Damn, there is actually a line of code instructing the uninstaller to delete the settings. Sorry about this. I opened an issue on GitHub to discuss whether we want to change it in future versions.