TL:DR Make it clear that a profile upgrade is going to happen.
When a newer version of Joplin is published clients display an upgrade available message with details of the changes. When the new version upgrades the "profile" would it be possible to clearly add that this will happen and that the user will not (easily) be able to revert to their current version? A search of the forum shows this this has caught people out quite a few times.
This however would not be seen by those who manually download and upgrade. So alternatively would it be possible to get the installer and AppImage script to let the user know that after continuing with the installation they will not be able to downgrade? I am thinking that this may be of benefit to those who download pre-releases for testing believing they can revert if they want to. More often than not they can revert because "profile" updates are not that common (although there have been two so far in v2.14.x!). Just trying to think of a way of preventing users from getting a surprise after they have installed the package, especially a pre-release. I realise that anyone wanting to test a pre-release should really create a test environment rather than use their "live" install. However not everyone will, or they may not even be aware that this may happen because it is not mentioned anywhere or is only referred to obliquely in the changelog for a pre-release ("Improved: Migrate profile in preparation for trash feature (115eb5d)").
Of course whether the user actually reads the message is something else 
The term "profile" now has two meanings (sort of). There are the user, or personal, profiles that users can switch, and the app, or Joplin, configuration profile mentioned above. I realise that they are basically the same thing but the error message use of "profile" may cause the user to start hacking about with their profile folders / configuration to get Joplin to start which is not the aspect of the profile that is causing the problem. So could consideration be given to renaming the app "profile" to something else (database?) so that when a user gets an "Unknown database version" error it will not lead them astray!