@Alain_Hamel: Not really sure since it’s hard to replicate, but it could be that the level names in your files are just different. The families already inserted stay linked to the graph: they are not erased but rather created in a new location each time you re-run it. To duplicate elements, just use Family Instance By Point in Transaction from Bakery. Another tip that could lie in the thread you mention is to run the graph once, disconnect the Family Instance node, re-run (the objects will disappear from Revit), then undo in Revit (the objects will re-appear but disconnected from the graph, no blue point anymore). Then reconnect, change parameters and re-run.
I have another update to this topic, since the error still occurs in Revit 2021.
I use the “Set Location” node at the end of my script with a pass-through from Clockwork.
Regarding the issue where elements are being deleted, this has to do with “zero-touch.” There is a lot of information on how this affects elements. The basic issue is, that if you run the script and place elements, those elements are stored within script and maintained there. In order to avoid this, you have to build a script which works and don’t save after executing. The more simple solution would be to run the script through dynamo.