I left Cherry in my house, while I went to save some people from Big Town... and when I came back she was gone but back at Dukov's Place.
I could not get her to follow me anymore because the option wasn't there.

I've found this: http://au.gamespot.com/pc/rpg/fallout3/show_msgs.php?pid=918428&topic_id=m-1-47890619#msg_id_m-1-524491220

But
Set MS14.CherryOffer to 0
Set DialogueDukovsPlace.CherryDeal to 0
Set DialogueDukovsPlace.CherryGone to 0
-
GetQuestVariable CherryGone (if it works, to see what it is)
SetQuestVariable CherryGone to 0

All give syntax/compile errors.