I tested out Jordan's most recent version of the merge concepts module (see here:https://tickets.openmrs.org/browse/TRUNK-2351), and noticed that it does not work correctly when it comes to answer concepts, which are stored in the value_coded column.
When i tested it, the module cited that the obs count for these two concepts was 0, even though I knew through my own query that there were several instances of the two concepts in the value_coded column of the obs table. It appears that the module is checking against the concept_id column of the obs table, which works if the concept is a question. However, because the concept may be an answer to a question, it also needs to check against the value_coded column of the obs table. When the merge was completed, I saw that the entries in the value_coded column remained as they were originally.