The way of resolving replication conflicts recommended by official documentation is:
_conflicts field (e.
The best solution would be to use the reserved property _deleted to remove documents instead of HTTP DELETE. Then you are free to also set other properties:
doc._deleted = true;
doc.deletedByUser = true;
doc.save();
Then in the merge process check the _changes feed for _deleted_conflicts and delete the document if there is a revision within _deleted_conflicts that has the deletedByUser flag set to true.
I hope this helps!