I think that you DON'T mean to place ".cfg" or ".ini" files themselves into the DB, just the info.

I don't know how many config files that you have. Text based config files are usually (in my experience) "small" some hundred or so lines, not thousands of lines.

I suspect that this evolution will need to happen in steps at least for development. Sounds like you have 2 main classes of applications. Ancient legacy ones and ones that are still under development.

I don't know how you parse these config files now. But I would be thinking about modifying the "under dev" programs with an interface that like a DBI, even if at this stage, a flat file is underneath that.

Depending upon how well or not well the info from these config files has been organized and accessed, this could be easy or very hard. You would want to standardize terminology for say "student_last_name", etc.

Then work on the Database. And then how to export config files to the other legacy applications.

A HUGE THING that I am missing here is the application that replaces all of the individual config file edits. I think that this is where you should start!

So to amend my previous thoughts, I would design the user interface for this "global sys admin" application. Then work on the individual apps.