Database merging and pruning

I have maintained a small local instance of erpnext starting with version 6 then 7 then 10 then 11. Trying to clean things up to insert data into version 13. Due to migration issues in the past I have the first year separate from all years after that. I hope to recombined them for version 13. I made sure both dbs are on the same version 11 branch and exported to .sql files. Reviewing both schemas (in phpmyadmin) show differences and unused tables. How can I get then to line up with each other (schema wise) to allow merging the .sql files?