The searches should be:
Code:
https://archiveofourown.org/works/(\d+)
https://www.fanfiction.net/s/(\d+)/1/
With the replace:
And set the identifier to "ao3" of "ffnet" as appropriate.
The above will add the identifier. If you want to remove the URL identifier, you should do the search again, but with nothing in the replace field, and "url" in the destination identifier.
To limit it to just the stories that are not "In-Progress", search for the books before doing the search-and-replace. That should be with:
Code:
not #fanficstatus:"In-Progress"