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I use calibre to make my own ePubs from various sources. Once the ePub is finished, I remove it from calibre, and manually copy to the eReaders and to a location I use for archival purposes.
This way I have a full control of what's happening and if something goes wrong there is only one solution (copy back from archival media) and one offender, ME and only ME.
I don't know calibre, but my lifetime experience with software told me that almost every software has issues with long lists, and also make my life difficult in finding a certain book among 2000 others, even with filters and selections and stuff.
Keeping the things simple is one of my life commandments.
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