I wrote a program to generate my database interaction module, so - when I change my database structure, I just hit a big generate button and the code is up to date.

PhpEd autocomplete doesn't seem to pick up my new variables and functions for a random amount of days. Obviously because the files have been altered outside of the program.

Is there a way to refresh it?

I've tried refreshing the workspace, but Also tried closing down and going back in

You have to open the file you generated to get codeinsight data refreshed with its new content.
PhpED does not scan all the files at all "possible" events, or it would spend too much resources doing so.