From your post, the following should give you what you want, you'll need two smartlists:
The first will list all duplicate albums found in both locations:
([filename (path)]="lossless" or [filename (path)]="lossy") ~dup=[album artist (auto)],[album]
The second will list all files from both locations, then discard any tracks that appear in the first list. That should leave you with a list of lossless files that don't have matching lossy partners.
For this second list, copy, and paste, the blue text into the "import/export" dialogue of the smartlist wizard and press OK. Next, press the "Add new rule" button, pick "Playlists" from the drop-down on the left, pick "Is Not Any" from the drop-down in the middle, and pick the first playlist from the list on the right, and finally, press OK:
([filename (path)]="lossless" or [filename (path)]="lossy") use smartlist wizard here
Now, I used the "lossy" tree in the second list also. My thinking here was that if you have been meticulous, there should not be any lossy files that do not have matching lossless partners. This list will contain lossless files that don't have a lossy pair, and also, lossy files that don't have a lossless pair.
If you'd rather concentrate purely on the lossless folder, then use the following blue text instead:
[filename (path)]="lossless"
and then add the playlist exclusion as described above.
That answers your question, which brings me to one of my own...
Did you know that MC12 has the ability to seamlessly manage a cache of lossy files specifically for use on portable devices?
With your device connected, explore the handheld options in MC.
You can specify a location and folder rule for the cache, you can specify a conversion format plus quality settings for the conversion.
You then sync the lossless files and MC converts them on the fly, stashing them in the location you specified ready for use next time you sync.
By default, the converted files are not shown in the library, so there's no duplicate clutter to worry about, and there would be no need for you undertake this task as MC would simply manage it for you.
If you knew all of that already, could you share the reason you don't use the feature? It works well for me, though really, I only use a single device.
-marko.