I did a few experiments right now and I found a way to reliably trigger one incarnation of the problem(I'm using kubuntu 18.04 in case that matters):
- unsubscribe from all mods
- delete "launcher-v2.sqlite" and all files in the "Paradox Interactive/Europa Universalis IV/mod" folder
- start the launcher & exit it again
- subscribe to a mod on the steam workshop (I used Simple End Date Changer, because it is tiny)
- wait for steam to download the mod
- start the launcher
- click on playsets (the mod should be there and automatically be enabled)
- exit the launcher again
- unsubscribe from the mod in steam
- start the launcher
- click on playsets (the mod should be there, with a red triangle and the message "This mod is not present on disk.")
- exit the launcher again
- subscribe to the mod in steam again
- wait for steam to download the mod
- start the launcher
- click on playsets (the mod should be there and still be enabled)
- look at the "Paradox Interactive/Europa Universalis IV/mod" folder and notice that it doesn't have a .mod file
- click on home and on play and confirm that the mod is not active (the checksum in the main menu is still "5d62" and in case of the simple end date changer clicking on single player and entering a year after 1821 and confirming with the return key makes the date jump to 1821, but not beyond that[if the mod would be active, dates till 9999 are possible])
Probably not all of these steps are necessary. And there is at least one more way to trigger the problem(by just deleting a .mod file for a subscribed mod), and I guess that there might be more bugs or circumstances which might cause the same problem.
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