As the name implies, amputations are permanent. Amputations were added primarily for game dev / exporting to a real time rendering environment, where many extra bones are that are not being used is just a performance drag. There are also maybe 50 bones for hands that can sometimes go as well. Manually deleting bones causes problems for Blender exporters, since the matrix weights are not reset to the first bone NOT deleted that way.
I think in some poses that there must be some face poses changes or the order in which things occur on the MH side, causes problems changing poses, & transferring expressions when not standing. I tried and could never expressions to work no matter the pose, especially 'Flying'.
One workflow which you may try is getting all the expressions you need across early & put into shapekeys, then ditch the face & or finger bones. That way, you could get into an expression, later independent of any poses or head bones. Syncpose is tolerant of bones that are no longer present.
- Transfer model standing up. Expressions transfer best then.
- Remove any modifiers which change vertices, (subsurf, hide face). They prohibit shapekey creation.
- Uncheck 'No Location Translation' to get the best expressions. It is an old option, which probably should change default or even be eliminated in future.
- Transfer expressions to shapekeys.
- Amputate head.