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You can get round it by only checking out either .epubs or .pdfs which is a bit of a pain but I find this easier by making extensive use of my overdrive library wishlist which shows which format books are in. I build up a long wishlist of books I want to read and then make sure I choose either 2 epubs or 2 pdfs at a time (my 3rd choice is always an audiobook) so there are no conflicts.
I don't think there is much you can do about it just a known bug unfortunately.
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