Do you have a backup file from just before this issue was observed? If so, restore it. That is likely the fastest and easiest fix for this issue.
Also, when you reauthorize any accounts (or even if you change an account's connection method, Reset Account or deactivate/reactivate an account) always make sure to look very closely at all of the information if/when Quicken asks you what to do with the data that was downloaded. It seems something has happened causing Quicken to not match the downloads as reliably as in the past. The result can be an issue similar to what you describe.
You are correct that changing the account names does nothing….they are just account names. Once an account Type has been changed it cannot be corrected or "fixed". This is why I suggested restoring the backup file (from before when this problem started). Did you try that and what was the result?