How to change data structure in mysql using mysqldump without deleting files
As long as you don't rename tables and columns and you are not using partitions you might use schemasync .

Basic usage is:

schemasync mysql://user:pass@dev-host:3306/dev_db mysql://user:pass@prod-host:3306/prod_db


This will produce two SQL scripts - one for "patching" the production database, and another one for reverting the changes.

Please note that schema altering will lock the tables being affected, so you will have some downtime anyway. There are tools to avoid this: pt-online-schema-change from Percona and oak-online-alter-table from openarkkit.

Also, as with any possibly destructive changes, test the procedure on a staging (or other non-production use, but production data and schema) database.