Your 'temp' tables need unique index using 1 or more fields as required. Each time run append query in vba where you turn off warnings, run append query, and turn warnings back on. If doing that, an error handler is strongly advised so that you ensure warnings are turned back on. Now you'll only get new records and the operation will be 'silent'.
Or set index as noted, run the query/queries manually and deal with the warnings - there will be at least 2. One warning about appending, one about how many records could not be appended due to integrity violation of some sort. That can be unnerving for some users but you'll get only new records in your table.
The more we hear silence, the more we begin to think about our value in this universe.
Paraphrase of Professor Brian Cox.