I don't have any old projects with wah guitar recorded this way, but I did save my test from this morning. When I open that test project and hit play, everything plays back as it was recorded.
I can make changes to the amp settings, speakers and cabinets, rooms, etc. with no change to the recorded midi wah playback.
I can bring in other pedals, change their settings, and their order in the chain ONLY in the AT5 window that shows the entire signal chain (on the bottom). However, if I replace the current wah with a different one, the recorded wah midi information no longer plays back and the new pedal doesn't move in the "gear view" window.
Additionally, if I add any pedals in the "gear view" window, the recorded midi will no longer playback.
It seems that changing the wah or changing anything in the "gear view" window cancels out the recorded midi. The midi information is still there and the wah pedal still "moves", but there's no audio of the wah information. Replacing the wah pedal with another cancels the audio and the new wah doesn't move; although, the midi information is still present on the track.
My AXE I/O is version 1.2.1 2A21, and I've never updated the firmware.
Maybe watch the video again? Maybe you missed something.
If you'd like me to look at or test something else, please let me know. I love midi but know very little about how it works, which is why I love TheSuperFunAwesomeHappyTimePedalShow video.