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Nickel uses a database for settings. If your PDFs are behind a hidden folder, and no entry exists in the nickel database, for that PDF, nothing Koreader does to that PDF should have any effect on Nickel. By "When closing Koreader and returning to Nickel" do you mean that you don't return to KSM when you close Koreader, but are returning directly to Nickel? Are you using KSM's options to set that up so you can switch between then directly?
Luck;
Ken
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