I think barriers could be one way. Unloading the enemies if you move far enough away or despawning the bullets after they leave the screen could also work. Depending on the game and style, locking the player in the boss room also comes to mind. Level design was pretty cool, by the way. I found it kinda maze-y, but not frustratingly so. I didn't have to backtrack a mile if I went the wrong way, but I DID have to do a bit of exploring to make progress.