Gavin,
I must apologies I had made a mistake. I can replicate your issue such that you get 2 AXF files not one when one layer is checked out and the other is a read only layer. So I can't back track fast enough! 😮 Yeah looks like you cannot achieve what you were looking for just 1 AXF file. But in my experience the more you jam into it the less stable it becomes and the device crashes more often. I do what you are planning to, I have a layer checked out that I'm populating and everything else is read only shapefiles.
Duncan