I have a user.js file that I place in my non-PortableApp Thunderbird profile directory. When I run the PortableApp version of Thunderbird, I place that same file in:
C:\ThunderbirdPortable\App\thunderbird\defaults\profile
Unfortunately, the changes detailed in my user.js do not appear in the PortableApp ThunderBird. Does this version of Thunderbird not support user.js files?
Your profile is in the Data directory. Data\profile to be precise.
The App directory is for the application as indicated in the readme.txt contained within: "The files in this directory are necessary for Thunderbird Portable to function. There is normally no need to directly access or alter any of the files within these directories."
All the portable apps follow these directory layouts. All user data is contained within Data.
Sometimes, the impossible can become possible, if you're awesome!