Use reload book in the viewer controls to reload the book. And the code has th eability to invalidate caches on code changes (not version changes), but I use it sparingly, since it invalidates all caches, imposing large performance penlties on everybody. In the case of comics, I dont think it is worth it, since the calibre viewer is not really designed for comics, in fact IIRC by default calibre does not even open comics in the internal viewer.
The cover being different betwen what is in the library and what is in the book, has always been the case unless you do polish/embed metadataconversion after changing the cover inthe library.
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