Thankfully my outer torpedo doors were closed while under attack, and I could remove the eel from tube 4. However, Bernard, leading the torpedo detail, then loaded it back in for me. While Bernard was in the john, I then instructed the team to unload again, this time ensuring that the 1st officer locked Bernard in the bog. (Switched off the auto-load function). This way, I've got my torpedo back, which was subsequently used.
Thanks for your advice!