Hey Jordan,
to be honest - I can't remember. This was more than 3.5 years ago.
But I guess I couldn't find a reason or solution for this.
I just don't try to better name the custom fields to not need to rename them afterwards.
Never again tried to rename custom fields due to the problems I constantly had then.
If I were in your situation, I would probably import a backup to get everything up and running again.
If you still want to rename the fields afterwards, simply create a new one and migrate the data to the new field. You can then delete the old custom field.
However, this has the disadvantage that you will have to make some changes to the website. Maybe this works via search & replace in the database. But I never tested this.