I went through the same thing a year or two ago.
If the stories haven't been deleted, FanFicFare plugin might be able to help. If I remember right, my method was similar to this (though I did re-download as ePubs):
1. Import the PDFs.
2. Convert it to text. (Don't worry with messing with settings trying to make it look pretty, you'll be deleting this.)
3. Set up FanFicFare with the columns. I highly suggest creating a longtext saved metadata column.
4. While doing this, make sure "search inside books for story URL" is checked.
5. Run FanFicFare update on your imported books, with the "download metadata from website."* Hopefully, FFF should find a story URL inside the text file and then download the metadata from the site, assuming it haven't been deleted.**
6. Check that the metadata went to where you expected it to. If not, change the settings and try again -- if you set up the longtext saved metadata column, you can use the "update from column" option to save time.
7. Once that's done, delete the text file.
* I would avoid doing this on more than maybe 5-10 fics at a time to avoid hammering the site.
** If it's been deleted, you'll probably need to enter the metadata manually.
If you need help with getting FFF set up, the plugin thread would be a better place to ask.