Normally the only thing that could change in an ME-1 with a scene change on the system would potentially be the channel name, and that would only apply if using the auto channel naming option in the ME-U.
How is your patching saved in the scenes, as far as being “scene safe”, is anything changing for those 2 affected channels.
Beyond that I have no clue why a scene change would change a group config on the ME-1.
The only signals out of the system should be audio, channel name, stereo link status.
If the stereo info changes, that might could cause an issue, but I can’t say for certain.