This is also how I do it. When upgrading there is always the possibility of a conflict between your SQL commands and the changes done on PEQ, but if you are lucky you will get warnings and you will read them ! At worst you will find out about the conflict when you play
Writing the scripts is not hard, but requires a lot of rigor. In the scripts I also precede each change with the command to "revert", or "delete" the change to ensure the script can be run as many times as you need.
Ideally what would be needed is a bit of tooling for this : a tool that starts from a fresh PEQ install, applies a few specified scripts with widespread effects (see below) and then compares the modified-PEQ with your current database and outputs the proper SQL commands. That would be great.
You want to apply a few SQL commands to the standard PEQ first if you do general changes in the DB, like making all items droppable and such. Otherwise you would end up with a script changing every entry. The use of this tool would be to cope with micro-changes.
Anyone feels like writing that ? Eh eh...