• Only one main Calibre database for fiction and nonfiction.
Programming or books with supplemental data/source code are zipped and added alongside.
Used to keep comics separately >100mb per file as not to bloat the library, have so few I finally imported them.
Audiobooks are still separate, I make "backup" with InAudible into individual mp3 chapters. The one filetype limit per book in Calibre means I create a m3u playlist and link it up. If I started today I'd create single m4b instead...
• Epubs, etc are already compressed. I was sorting by Author/Book before and if I ever wanted to abandon Calibre I'd just strip the Ids and be done. 10 years later still using Calibre!
• Filename when imported already avoid characters/symbols/lengths incompatibilities with other filesystems.
• Column and other customization can be backed-up. Title, Tags, Description are saved in both the metadata.db and individual opf files.
• It's recommended to use a local hard drive, networks drives at your own risk.
I have Calibre running on a server that takes regular snapshots (ZFS) and sent offsite, most modern OS can do similar. Although OneDrive, DropBox, etc might lock files and create a
mess.
My server has a GUI, but you can also manage remotely with Calibre's server or something like
calibre-web.