There is a serious flaw in the mechanics of boarding & capturing a smaller vessel.
In attempting to transfer from a sinking Trincomalee to a healthy Snow, I found I had lost 90 crewmen between the end of the boarding and capturing. Assuming I still had my original complement, I grappled another Trin after firing a broadside of grape into her. Needless to say, it didn't turn out well.
I suggest players be given a choice of transferring the entire crew or taking her as a prize and transferring a prize crew, retaining both with reduced operational capability.