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that makes sense, so why not just keep everything as-is. A good syncing program will only take a few seconds to spot that nothing much has changed so your re-synching speed should be unaffected, and like you say - ebooks don't take much space ?
syncing: i use freeware freefilesync. When I re-synch my book or my mp3 collection it only needs a few seconds to deduce that 99% of files have not changed since the last sync. (the synchromagic shareware solution that I used to use was much slower at that ).
if you split your library into two, by format, then you will duplicate much of your metadata & thus using more space ?
as a test, I'll time running freefilesync for my calibre library, and synching to 2 backup locations: dropbox and to another external drive location. So, i launch the program - there is a a few seconds wait for the external drive to spin up then it counts up to ~28,000 items checked, and copies a few recent changes, all in ~30 secs. That's for a 2+ Gb calibre library which holds a mix of formats
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