> I"m not sure what you're looking for. Do you want to see the files that created the database?
?! No, the result of executing the sql command Show Create Table <tablename> on each table manifesting the problem you report, so we can begin to understand what's happened. Also what OS is this running on, is it on your machine or hosted somewhere, if it's your machine how much RAM is there?
> worked just fine for years, just started acting up a couple of months ago.
You say that as if you expected it to go on working forever. If software could be perfect, that might be possible. MySQL 4.1 is way obsolete, near 15 years old. Software isn't like architecture, it's more like wine, turns to vinegar with age---you need to upgrade MySQL, and there'll be some pain since you've missed five major versions (5.0, 5.1, 5.5, 5.6, 5.7) and you're about to miss a sixth (8.0).
To get yourself up to date, for each major version you'll need to mysqldump your entire database, install the new version, import the database, then regression-test the db and your app till everything works again.
If the db is simple and small, you might get by with jumping from 4..1 to 5.7 by deeply massaging the dump file, but you'll need a lot of knowledge you apparently don't have re the incompatibilities between your 4.1 database and current MySQL formats and methods. To get a feel for what you'd be looking at, you might have a look at
https://www.artfulsoftware.com/infotree/mysql_incompat.html.