In my experience, when you export a database (through phpMyAdmin for instance), part of the SQL script that is created includes a "DROP TABLE IF EXISTS 'table_name';" before doing a "CREATE TABLE 'table_name'...;" to build the new table.
My guess is that this is not what you want to do! Certainly use the dev system to alter the structure in order to make everything correct, but then look around for a database synchronisation routine where you can provide the old structure, the new structure, and the software will create the appropriate "ALTER TABLE 'table_name'...;" scripts to make the required changes.
You should then really examine these change files before executing them on the live database, and of course BACKUP the live database, and ensure you are able to fully recover from the backup before starting any of the alterations!