It is normal, I have just created some new COMBI patch and are full forking.
COMBI work with the first 8 midi CH, from CH 1 to CH 8.
When you are in EDIT mode, you are eiditing this 8 midi channel, you wil lose the al midi setups of the last combi patch.
When you exit, just select one atother COMBI patch and then recall again your last created patch.
In this way we initialize again the all 8 midi channels.
The Global keyboard transpose have nothing to do with the layers transpose.
When you change the gobal transpose, will also setting the new transpose for the COMBI and for the all other sounds engines.
Try it, you will see that is working.