It's best to check your stock/bin list see what the reports show you have in stock, if you have a bin location with alot of no stock parts and very few parts with stock against it, you can go into the individual parts records with stock and move them to a new bin location via the parts record> stock tab.
Then once you have a bin location with no stock parts, within Parts Managers Toolkit> Set up> Rename Bin list, you can change the bin location from e.g ABC123 to NOT STOCKED and this will remove them from displaying in the daily stock, no stock report and stock orders.