Thanks for your rapid response!
I rely on shortcuts because when I install Windows games I don't have them create an entry in the Start menu. I also have some indie games which don't appear in the Start menu, and I don't have a Steam API key which is needed to use the Steam import option.
My workflow is as follows:
When I initially import my Windows games into Launchbox, I use the Wizard from Tools > Import > ROM files > Single Platform, then add my shortcuts folder, at What platform are you importing games for? I select Windows from the list, at What emulator would you like to use? I leave that field blank, at Would you like to move or copy the files? I select Use the files in their current location, at Would you like to download metadata for your games? I leave that ticked, on the next three screens I select the metadata I want and set any custom options, then Launchbox lists the shortcuts it found in the folders and I click Finish.
After this, if I add any new shortcuts to the folder, that is when I use the Scan for Added ROMs option.
Wouldn't it be possible to flag the games as Windows instead of ROMs when Windows is selected as the platform and the emulator field is left blank in the import wizard, and not set the use emulator flag?