I'm having the same issue. My ebooks are stored in /storage/emulated/0/Calibre_Companion/; when I try to open with Nook reader it's looking in /storage/emulated/0/NOOK/copy/. Cool Reader is looking for /external_files/emulated/0/Calibre_Companion/. Just started happening recently. Haven't found a solution anywhere. Anyone have a solution for this?
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