I had the same problem and solved it with a simple fix. I added a Yes/No/blank column called MetaFix. By default, that column is blank. When I clean or fix a book's metadata, I check that column and turn it to yes (a green check mark). Now, if I have to close Calibre, I can simply sort on the MetaFix column to group the books for which the metadata has not yet been edited.
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