Please note that Metadata Navigation and Filtering and Managed Metadata columns are different objects in this topic.
Using Metadata Navigation and Filtering is actually a way to bypass the list/library threshold since it is more about filtering. “Automatically manage column indices on this list” option is selected by default via metadata navigation settings. ...
Go to term store management tool -> Select the term set-> In the general section, check whether you set owner in the new term set -> In the intended use section, check whether click different use cases.
You can wait for a while, delete managed metadata columns and re-create again.
TaxonomyHiddenList is not already updated.
Depending on the amount of site collections in your tenant this can last longer than you exspect.
Just wait until the job has been done. This is a backend process and as far as I know you have no control over it.