Those files should be in Trash.
The problem is, you CAN undelete the files BUT
Calibre does not know to add them back to the db.
SO
Once you have done the undelete, you need to
1) create a New Empty Library someplace else on the drive (right click the Library Icon) NOTE if you have custom columns, use the
COPY STRUCTURE option
2) Once the library is done, switch back to the old: Select All (ctrl-A): right click Copy to Library (the new one): delete after copy. This moves Known Books.
What is left in the library FOLDER is lost books
3) Switch to the new Library: Right click
Add :
Add from Folders and Sub Folders: <point to the old library folder>.
That should do it