Ah now I am very confused. Did you change the level design? Every room I need to go and DID go in the last version (my map shows I have been there) is now ability gated by needing to be in ball form... I only have missiles and high jump. So I have no clue where I can go now.
I DID download it after your last comment. Did you update it a second time? It didn't break my save, I continued exactly from where I was. Do I need to restart?