kovidgoyal, gbm - thanks for your suggestions. I tried the latest Calibre binary version 2.82 64bit which did not connect to the PRS-650 as well. So I downgraded the kernel to 4.5.5 and voilą - it works. So it definitely is a kernel-issue.
As the 4.5.5 kernel did not work well with my desktop environment I will stick to the latest kernel 4.9.13, but at least I know that it's solely the kernel.
@kovidgoyal I wonder if more users of Calibre will experience this problem when the relevant kernel update e.g. ships in Ubuntu which is much more wide spread than Fedora - what do you think?
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