Curious, what method do you use to download your fanfics?
For the past 2-4 years, I've been getting most of mine through AO3 because the built-in epub download is so convenient. I save fanfics directly to Dropbox for immediate reading. All the metadata editing though, I leave for later via Calibre. It took a few months of tweaking but I have a pretty decent Calibre workflow for AO3 now (mostly lots of saved searches and bulk search and replace).
Granted, I'd sometimes have several months worth of unorganized fanfics when I'm too lazy to fix the metadata in Calibre. Mind, I'm even lazier fixing metadata on Marvin anyway so no big deal. It's a major pain having to enter all that info manually.
Marvin
For what it's worth, Marvin does allow backup of the library and database via
General settings -> Advanced -> Backup and restore
Alas, you'll need to figure out how to convert from Marvin's SQLite database to something importable by Calibre. Another thing, it backs up the entire library every single time (although given what happened to your iPad, that might actually be a good thing).
There used to be better integration between Calibre and Marvin (Classic). Unfortunately, I believe Apple killed the method that Marvin used post iOS 8.
FanFicReader plugin
Alternately, as long as the story url is located in the EPUB somewhere, you might be able to use the FanFicReader plugin to scrape metadata from the fanfic website (assuming it hasn't been deleted from the site yet).
Calibre Companion
Thus far, I believe Calibre Companion only has the ability to update read status. With Calibre content server recently having added metadata editing support though, mayhaps @chaley could chime in regarding feasibility of adding similar functionality in CC.