I think you are right about this, I was never really happy about the current method, and it could do with reworking, and to be honest I didn't anticipate network drives.
What would you think of the following :-
1) Add the root folder containing multiple TV Shows
2) Loop through the added shows, if a TV Show contains no nfo file then create a blank nfo, and Scrape only the TVDBID, then prompt the user if there is more than one entry.
3) If the nfo exists, but is missing a TVDBID then as above but ammend the existing nfo to include TVDBID
4) Repeat 1-3 until all TV Folder Roots have been added.
5) Now that all the TV Shows have been added now the details, posters, fanarts, season thumbs, can be scraped automatically, with no user intervention needed.
The reason I think it may be best to do it like this is the time factor, already scraping information for TVDB, getting fanarts, getting posters, and from the next version, there will also be season thumbs downloaded to the folder. Using the above method people could add the initial tvshow details very quickly then leave it running on auto to do the rest.
On startup it would be easy to just ignore missing/offline folders. But the program would need to be restarted if the drive was later added.