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Originally Posted by Sparkling
If I understand correctly using option #2 you may still change collections manually - they are just not synced to the calibre library? If I've misunderstood please correct me and ignore the rest of my comment 
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Yes, you may make changes manually. Neither option includes syncing back to the calibre library, but that doesn't change the validity of your arguments for option #2.
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As banjomike mentioned, option number 1 seems ineffective. [...] Having the deleted collections pop back again is more than a little troubling so alternative #2 is definitely preferable for me
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So far, 100% in favor of option 2.