First off, discoverning portableapps has been fantastic! Thanks to all who make this possible!
I have been placing my custom python plugins into KritaPortable\App\Krita64\share\krita\pykrita. This has worked well until I recently ran a newer portableapps installer to upgrade Krita, and this removed my plugins.
I then tried to place them in KritaPortable\Data\krita\pykrita, but my plugins have disappeared from there as well. It seems that this folder gets emptied automatically or something?