I'm not sure. One of my goals for the next map is to make it less prone to glitching like that lol.
If you beat the ice boss in the ice area, and looked into the eye and it didn't do anything, go ahead and go into creative mode, get a redstone block, fly behind that eye of ender and just activate the command block line that should be there. I think that might fix it, but I'm not sure, haven't looked at that map for ages.
By destroy the bosses, do you mean the last boss? Because if that isn't working, then I really don't know. Glad you seem to be enjoying it though!