Mixing License Codes and the Mac App Store
If you see this alert, it’s because you previously purchased a perpetual license from us for the current major version of BBEdit, but have since installed and begun using the same major version of BBEdit from the Mac App Store.
However, this can also happen if you have ever purchased BBEdit from the Mac App Store. In this case, the app store remembers that you previously purchased BBEdit there, and then will forever replace your installed version any time you install updates via the App Store — even if you were already using a copy of the app downloaded directly from our web site.
A weird but probably not so uncommon edge case. Some apps can detect a Mac App Store receipt file and use that to activate the direct-sale version of the app, but App Review doesn’t allow the reverse—except, I guess, for cross-platform subscriptions. However, you can avoid the problem of the Mac App Store overwriting your apps by hiding your purchase.
Update (2019-08-01): Kyle Hankinson:
I have the Mac App Store version of SQLPro accept license keys. This way if a user purchased from my website but the App Store version gets installed somehow, the user never even knows, it just keeps working.
[…]
From what I can tell, it’s allowed as long as you don’t direct the user to purchase outside the MAS it’s legit (same thing as someone signing up to Netflix or Spotify outside of their app).