In the attempt to fix this, that recipe is lost until you level up.
Changing any other mod removes all Hyper Mods. So you can no longer make level 1 or your current level (as before the fix). When your level actually does level up THEN the correct level Hyper Mod shows up. At lower levels it's not hard to level up the mod in kills. But at higher levels it could take a very long time. So you are unable to create any Modules until you gain your next level.
I waited for quite a bit and the recipe never showed back up thinking it may show back up in 10 secs. It didn't. On that note, assemblers with your current Hyper Module recipe already selected stays. It will continue to work. But you are unable to change the recipe til you level up next. Also, on the far end, what would happen if this happens at super endgame. If the mod is Level 100, there wouldn't be any additional levels for it to level up and I wonder if the recipe will be lost.