Hey, I noticed this straight away at band practice tonight, it seems to only happen with presets imported from an older firmware - here's how to fix it.
Select your preset. Change to any snapshot in the preset to trigger the problem. Unplug your guitar cable (with your guitar connected - IMPORTANT) from the guitar input and plug it into the EXP2 jack for a second then unplug it. You should now see "EXP1 EXP2" in the expression scribble strip again. Click save twice before doing anything else. Switch to the next snapshot. Repeat for all the remaining snapshots in the preset. Finally switch back to the snapshot you want to be loaded by default when you load the preset and hit save twice again.
Your preset will now function normally in the 2.10 firmware.
The reason you have to keep your guitar connected to the cable is that you have to create a short circuit within the EXP2 jack and then remove it so that the Helix thinks it had an expression pedal connected for a second. When it sees that this connection was removed it will default the EXP2 function back to the internal expression pedal, thus solving the problem. This status is now saved with the snapshot which is why you need to repeat the process for each snapshot.
This solution definitely works on the floorboard Helix. I presume it will also work with Helix Rack but I don't have one here to test it on.
hefonthefjords's post in FW 2.10 Expression Pedal Question was marked as the answer