diff create a balnk data_merged when trying to solve conflicts automatically

I am having problems when I try to merge the databases. I followed the instructions like enabling revisions and always restoring the database when changes are made.

Then, developing new features in my site (on a dev box), I created a new node and in the production many new nodes. When I try to merge the dev and production database, however, I get conflicts. Hence, all right since I already got conflicts but never got problems like now. I tried with the two snippets the module provide:

1. When I try to resolve them with diff3 -e --merge ./databases/tmp/data_dev.sql ./databases/tmp/data_orig.sql ./databases/tmp/data_prod.sql > ./databases/tmp/data_merged.sql, I got a lot of production content stripped. (e.g.:my prod have 530 nodes and with this diff merge, it got only 230). I think this occurs because ./databases/tmp/data_orig.sql don't have any content inside.
2. When I try to resolve manually, the sequences are resetted to the development ones, then I got errors like duplicated entry when try to create a new node

Does anyone had the same issues?