OKAY you guys are gonna love the game again after I tell you this. I FIGURED IT OUT!
I solved the issue of the missing Chinpokomon.
The solution is to SELL ALL JUNK, leaving NOTHING in the junk tab before learning Nagasaki and the glitch will not occur. I just did some testing on this and it fixes the glitch. :D
If you're going for the achievement of not not selling any of your junk, beat the game first and then reload the game before going in to Clyde's fortress!
Sell your crap to get Shoe / Mouse-Tik / Beibersaurus to appear again!
The reason why this is so uncommon is because people probably sold junk their first play through and aren't really experiencing this glitch, so we're the early adopters of this crap.
I hope this helps you reconnect with the game again Shelledfate! It certainly did for me!
Peace boys. Mystery solved.
Wow, so relieved right now, I'm gonna do a 100% play through on my 360 now... I did the testing on the PC and it's definitely happening across all platforms.
XRizerX's post in shoe won't load at the last mission was marked as the answer