Well, I first discovered this as I was making my first portable app... PokerTH Portable (I saw the version on this website hadn't been updated (but now it has)) an easy way to make a newer version was simply by going into AppNamePortable\App\AppName and deleting the old files and replacing them with the new ones. I tried this with Frets on Fire and it also worked.
I also had tried this with Assault cube portable (from .92 to 1.0.2) but that didn't work. I'm sure what causes this but I know that the other two apps worked just fine.
As for the creators of the portable versions of those apps that need to be updated...
I know that the PA installer works when you try to package it but you will need to change the version number (appinfo) and recompress the files.
And for those who are really PO'd that those apps that haven't been updated, STILL haven't been updated, can still enjoy that portable app.
And if your not the original (for the lack of a better word) "portable-izer" of the app, don't update it, or John will get mad at you. *sarcastic grin*
Feel free to try this with other apps and say which ones worked...