At the risk of being told "I can download an older version of the tool" and have this topic be moot, I am curious, what if there was a different kind of gstool that's mainly for tile set conversion? (Maybe call it Gsconverter?)
How would such a tool work?
The newer versions should still be able to do this. They just cant save back to Lemmini format.
Can confirm: The newest version of GSTool still supports loading (Super)Lemmini and even Cheapo sets. It doesn't support Lix sets, but then again, it never has. (I also VERY strongly advise just waiting until the new-formats versions come out before trying to convert Lix stuff, for the simple reason: Lix uses piece names, rather than index numbers. New-formats will too. You're just creating complication by rearranging the set into an index-based one, only for it to be changed back a bit later.)
If these options aren't working correctly, report that as a bug (I did not re-test them). But they are definitely still there.