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OK, so I got home and played around a bit.
First, I do not have Time Machine turned on, so that shouldn't be effecting anything.
Second, I ran the library check and it found the empty folders and I used the "deletable" option to remove them.
I also had a couple duplicate formats, but more interesting, I had hundreds of "invalid titles" and one "invalid author", all of which were .DS_Store.
A quick internet search says that MacOS adds the hidden .DS_Store file to directories to preserve finder layout and other settings. This makes me wonder if the hidden file was added to all the unused author folders which somehow prevented Calibre from automatically deleting them after I redid the naming? Unfortunately, I deleted the empty folders before I dug into the .DS_Store issue.
I tried adding the .DS_Store to "extensions to ignore" field, but that didn't work, the check library tool still found all the .DS_Store files. I then added it to "names to ignore" and that successfully ignores it. After that I got a clean check.
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