Merge generated JOSM with OSM data conflicts

I have some official building plans that were converted to OSM format for a certain building complex. I wanted to have them replace the current buildings in OSM (and also add ones that weren't there yet) because they are more accurate. I wrote a short script that compares the buildings as shapes and then creates a JOSM file that replaces certain buildings that were deemed to be matches with my data. I then plan to manually clean it up and make sure it is fit for submission.

I want to be able to apply these this generated file to OSM. The file has additions modifications and deletions. If I open the generated file, then download the OSM data, it seems to merge them, but there's conflicts. If I try to resolve the conflicts, only the way is deleted, not the nodes. Any way I can have everything deleted (I have the nodes marked as "delete" in the JOSM file).

EDIT: Here's some screenshots documenting what's going on. http://imgur.com/a/yAYyo