I expect the data was extracted from ebooks (maybe using MultiColumnSearch Full TXT search feature) that didn't have the actual metadata embedded (e.g. book has jacket/title page with the info but not in the OPF file).
It's not just converting to HTML. The id tags is the important part as it tells the FanFicFare plugin which data should go to specific custom columns. There's no way to automate that without writing your own function (or a very complicated regex) and without the ids, converting to HTML is pointless.
Alas, manual editing to HTML might be doable for a few books. Not so much when you have to deal with hundreds or even thousands.
@Tanjamuse
Just a thought, extract just the StoryURL and let FanFicFare redownload. If any have been deleted, then just work on those separately.
Code:
Search field:
#your_source_metadata_column
Search for:
Story URL: (http[^\n]+)
Replace with:
\1
Destination field:
#storyUrl