Please ask in a dm for a link to the instance in the app. I have kept one corrupt reference (that if not deleted I cant purge the old class)
I have purged all other references.
When i copied and create or update object action node it triggered an incorrect reference to the old class in the new class.
I last week cretead a class. I wanted today to update the name so the node name would be better and more correct. In doing so the new almost identical class some how was mistaken to be the old class by the reference finder. Note that the number of properties I update or create are identical to before so it seems likely that since the schema is the same in the action node the reference finder thinks it is the same class.
I used duplicate action node and that led to some kind of wirering to the old class to be kept. In some cases I created a new action node and copied the property reference from the old class into the new and that also led to some kind of reference mix down the line even though the proprty I copied did not have anything to do with the old and new class.
As said i kept one corrupt instance that can be investigated so just ask in a dm.