If you haven't emptied the trash, I would suggest moving the deleted books to a new folder and then re-adding the books from that folder to calibre.
As for the remainder of your question, did you try a search on how to copy books from your device to a calibre library?
For instance,
will books transfer from device to calibre? was written about 12 years ago but still applies.
Have you actually tried to see if you can import the books from your Tolino to calibre by switching to Device view, selecting a book (or group of books), right clicking and selecting Add to library?
Note that you are likely to find that much of your metadata is likely to be missing in action.