I've never cleared in and then out of the BVI (back to USVI) with a change to the crew manifest. If they depart on the Roadtown ferry, I think you may need to accompany them to C&I so the crew manifest change can be noted, or perhaps you can handle it all when you first clear-in to BVI.

Also, I don't know of a convenient dinghy dock (short of wading ashore) near the Roadtown ferry dock if that's where you want to do the dropoff. You could dinghy to the Pub or TMM and from there it's about a 1/2 mile walk.

If they return from St John, then you should be able to both clear-in and clear-out of BVI when you arrive to BVI since you are on a charter vessel. You could all then clear into USVI using the ROAM app if all US citizens (CYOA will have the vessel info for you), or you dinghy to the Cruz Bay C&I office to clear-in then walk the 150 yds to the ferry dock.

As George notes, it really comes down to your cruise plan. If it means 1 less day in the BVI, then I would return to St John and spend an extra day enjoying the south shore anchorages of Lameshur and Salt Pond Bay, or add an evening dinner in Cruz Bay.