Your add-in should delete any toolbars it has added to PB when the add-in shuts down. This will remove them from PBToolbarConfig.ini. The next time PB is started, the toolbar should be created again when the add-in starts up.
Thanks for the reply. It seems that when adding my own code, I accidentally removed "IsCommandBarAdded = True" from the OnConnection handler. It is working great now!