The following issue "The Merge Agent failed after detecting that retention-based metadata cleanup has deleted metadata at the Subscriber for changes not yet sent to the Publisher." has been addressed with a workaround that seems to do the trick. Updating column cleaned_unsent_change to false insysmergesubscriptions on the Subscriber does indeed allow replication to continue.
However, we would like to know if this problem has been fixed in a Cumulative Update since SQL 2008 R2 SP2? Servers with SP2 installed continue to have this problem. Thanks so much!