OK, found the secret. Both the old and new part have to be in the mine parts bin at the same time otherwise when you try and save in the new parts editor the save button is greyed out and you can only save as a new part. This works as desired (you may want to make sure you have a backup of your fritzing parts directories before trying this, I do it as a matter of course before trying anything like this ):
load the 10440 part from above, and drag in a 2 pin connector from core and connect them to set pcb traces. I have a sketch with this done, but the 10440 part is preloaded and thus doesn't work, (probably because it will be in bin temp not mine). Now from core, search for battery and parts edit the 2 AA cell part that the 10440 was cloned from and save as new part (so there will be two of them in mine now the 10440 and the clone from core). Now in pcb view do the parts edit on the 10440 part and click on pcb view then file->load image for view for me the directory is
(although it was somewhere else in a parts factory directory on a previous try) which contains:
(I'm not really sure why so many files, but it doesn't seem to matter). I double clicked prefix0000_4e5dc67f03b72b14781f9bff55e9f212_1_pcb.svg which loads the different pcb from the core battery in to PCB. Now file->save (as opposed to file->save as new part) is also active and when clicked asks for a prefix (where I used the default and clicked ok) and then it prompts that it will make non reversable changes to the sketch. Clicking save changes the part on the pcb to the new (now broken) footprint although on a closer view I see that it is broken. I hope on a part with an identical footprint and connections the connections will change correctly. The secret appears to be having all the files in the same parts factory directory, so probably starting parts editor then manually copying the file you want to add in to the directory parts editor displays outside of fritzing will also allow you to substitute the files maybe (it may have more state that isn't visible from the creation of the parts in the mine parts bin though).