To clear the Phantom Pins you have to Delete the chips that are still active in file manager.
Step 1: Press the "Edit Chip" button to open the Store location for all of your chips
Step 2: There should be a Mismatch between the Chips in your hotbar (in game) and the Chips in file manager. Delete Every chip that appears in file manager and that DOES NOT appear in your hotbar.
Step 3: Do the same for the chips inside the "Wirelayout" Folder
Step 4: Reload the Chip and the phantom pins should be gone.
This is what I do to clear phantom pins so idk if its going to work for everyone but its worth a shot. :D