That sounds like a work flow that is bound to cause issues.
While the the extract file might have only been 20 hours old the data is likely to have been a bit older.
In any case is their any reason you are not simply using the normal JOSM download mechanism?
With the further information you have given the picture is a bit clearer. I would point you to the POSM (see https://github.com/AmericanRedCross/posm ) project as a potential alternative, alas I suspect that they simply haven't thought the synchronisation part of their project really through. I would suggest that you should simply accept such issues as you experienced as not avoidable and live with having to work through any conflicts on upload (you can minimize them but not completely avoid). Further splitter is really a special purpose tool and likely not suitable for generating extracts as you need them, osmosis or similar.and others are likely better suited.