Here is how I remedied this issue:

1. I selected all the clips that had be logged without audio settings.
2. Used the "Export Batch List..." feature to create a CSV file.
3. Removed the logged clips from the project.
4. Imported the CSV file back into the project.
5. Captured the clips as normal (with Audio and Video)

That was all there is to it. The CSV file only records the Tape name, clip name, In point, Out Point and comment. Nothing more. So, the project doesn't know any better.
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