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(1) The files that calibre works with - on your device - are only those it maintains in the file structure that it builds onto your device. It should not do anything with the folder outside of that file structure. That said I do seem to remember where a poster had made those PNGs a collection in Nickel.
(2) Making them a collection might make them easier to find.
(3) You might have to copy the rotated file and delete the file from your device then re-add the rotated image file with the same name as the original file. It would then need to get processed by Nickel, before it would work again. (The actual "koreader.png" is not needed or used when using KSM to launch KOReader.)
I haven't used calibre that way, as "collections" are a Nickel thing.
Luck;
Ken
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