@Aziuth FWIW this message was changed recently. Here is how it will appear in 3.2
2023-06-19 20:26:49,756 Dropping a patch because it contains a previously known reference (id=‘p1002’). Most of the time this is harmless and usually a result of updating a model on one side of a communications channel while it was being removed on the other end.
We display this message for “completeness” sake, but it’s actually not usually anything to be concerned with. So to be honest, I think you are worrying more than you need to be, and can just forget about it.
If you really want to get rid of it, though, your best bet is to add both plots to the layout up front an then toggle their visibility rather than removing/replacing them in the layout.