I feel like I'm missing something. What does custom_dupe_nodes.validator.mapcss look like? Does it merge duplicate nodes?
I'm not seeing the behavior that I think you are talking about.
Specifically, I am not seeing the deletion of any nodes. Can you give me specific steps to reproduce? If a specific building is the problem, you can copy its OSM id via ctrl + c. You can then paste it in the steps to reproduce.
Example steps to reproduce:
- Download area for https://osm.org/relation/5522180#map=16/-3.7094/-38.5529
- Select way 1107484204
- Move node 10133457174
- Upload. See node <duplicate> disappear.