not on my phone now so i cna be less cryptic. The server code has nothing to do with the Database on the normal level. Updating the server code will only require database changes if it is specifically mentioned in the update. Those changes do not affect the data in the tables.
The only time you would lose your data was if you sourced in the entire database again next time PEQ released an update.
I would recommend creating some kind of process for your MySQL server to backup your custom bits though. It is never good to fly without a disaster recovery plan.
If you want to be able to resource a full DB and then redo your changes, it would be best to probably create a SQL script for each table with the insert/updates needed.
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