The relevant things are in the database; updating the plugin’s files won’t really do anything.
If you identify the differences between what you have and a “normal” set of tables for the plugin, you can plausibly manually make the appropriate changes. You can look at the upgrade function of the plugin to see what was added in what versions: the two columns you mentioned are among them, but also 3 added columns on the exhibit_pages table.
Making sure the structures match is easy enough, but the Exhibit Builder 2 to 3 upgrade is significant and makes many changes to the structure of the tables… not knowing where you encountered your issue or exactly what you did to resolve it makes it tricky to say with certainty if simply adding those columns will work. In particular the 2-to-3 upgrade converts your existing exhibit layouts to the new block-based system, and it’s very possible that if your original error occurred during that part of the upgrade that your existing exhibits would not be correctly present. You might be able to tell whether this is the case now, if you can look at the pages in exhibits.
In general, it’s not a good idea to update the version number manually in the plugins table, unless you’re sure you know what the consequences are.