Thanks for the feedback, Roger.
I think the files concerned are the remapped images only?
If this is the case, then it is a matter of defining what file is temporary and what not. If I check any of the boxes in the Remapped Images section of the Stitcher tab then these are not temporary files and the current behavior is correct. But if those checkboxes are unchecked then the images remapped by nona are temporary and the current application behavior is incorrect.
Can you confirm?