The current workflow is to manually add custom bones to the bone hierarchy created by the script. Since the script is not aware of these extra bone, regenerating the rig from that point on will delete the custom bones and you’ll have to readd them.
I have a few ideas on how to automate this process so the deleted bones are readded. I hope to add that feature in a future update. But for now the workflow is to finalize the base skeleton bones so you don’t need to regen the rig anymore and only then start adding custom bones to the rig.