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I cannot think of a particularly good way to handle a situation like this.
You might be able to perform a search with series:true AND secondseries:false. This would show you any books which have info in the series column, but nothing in the secondseries column. You would still have to manually slog through all the results, updating entries as you go. You can then sort on series or secondseries depending on whichever similar wording you're looking for at the time. I would think you might need to sort on both, just to make sure you don't miss anything.
You will still need a way to find and compare books where there is info in both columns though. Obviously setting both to true will get a listing and sorting will help to group similar series names. It won't be perfect and you'll still have to do a lot of manual editing.
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