Hi,
The only method I found that worked for me was to remove as many sailors as I can from that ship out of HQ. Then relog into game, open HQ again remove the hidden sailors and the ship. Otherwise you may have to put a ticket in to have them do a check upon the account to recover them.
Tips: I find the ship/sailor bundle tends to bug if more than like 4 ships in the HQ so possibly removing any other ships with crew will assist in seeing the crew members once more. Also going into page 9+ tends to lose BO's at least with my account. Good luck.
-Gen