Continuing that thought, if swapping the two files was your intention, you might
be able to get away with something like
 darcs mv A A-tmp
 darcs mv B A
 darcs mv A-tmp B

which reduces the risk of conflicts if you modify either A or B.  Now, the
question of whether darcs2 should handle these conflicts or not (i.e. without
taking forever) I cannot really help with.  For instance, maybe switching to the
darcs2 format would help.

I'll have to ask David when we have a few more details about what happened.