Not very helpful as an addition but I can confirm I have the same issue.
- HD PROX with FBV Shortboard MkII
- Mission Engineering pedal
- HD Amps installed
Second pedal needs to be unplugged and plugged in again every time a patch changes rendering it unusable in any practical situation. The change of patch also renders EXP1 inoperative on most / some occasions. I haven't done extensive testing though.
Not rushing to rollback firmware to check due to HD Amp pack but suspect you are right this is a bug in new firmware, given when the timing of when I noticed the problem and your reported fix. I am going to open a ticket, if others do the same perhaps it will be addressed as a bug.