Thank you for the detailed data; this might help clarify the issue.
I believe this error occurs when bus data exists but the corresponding .tres file is missing.
If you switch the bottom panel to Audio and use “Save As” directly under res://, the error should not occur. Could you please try that to see if it resolves the issue?
We fixed the template side half a year ago, so this issue should no longer occur with current templates. However, it might still happen if you are using an older version of the template.