I am also curious about this, however “Install BuddyPress on a secondary blog” don’t seem to answer the question, and “Yes” answers the question without an explanation or instructions.
Strangely enough, all of a sudden the groups came back.
Except now, it happened again. I was doing some admin work in the groups (clearing out the spambots) and then I lost the groups again. It says “All Groups (12)” at the top, but then says “Showing 1-9 (of 9 Groups)”. All I did was remove some spambot members. I have not updated or activated anything.