This comes up ever release. The sale price was too good to pass up, but the result is that itch doesn't recognize folks who purchased the game on sale as having purchase the full value release.
This is the only distribution platform that I've ever encountered this behavior. It might be worth including a notice about this issue in your release notification so folks are not confused and/or angry with you (who are not responsible for the shop failure) to have to deal with each time the game receives and update.
That being said, can you let us all know when those of us with a discounted full license will be able to access the update? I for one really like the changes and direction you have been taking this game.