Awesome!
Commenting out !market.getSurveyLevel().equals(SurveyLevel.FULL) &&
fixes up existing games mid-run. I built a ghetto .jar with the patch, but don't know how to build one properly so won't upload it unless people ask.
Wow I didn't even realize there is so many empty planets in already inhabited systems, because I never needed to survey these!
Spoiler
(https://i.ibb.co/3mddDT5/Screenshot-2.png)
Here is updated version that also fixes already surveyed planets:
Fix All Empty Planets v1.0.zip (https://bitbucket.org/Carabus/fixemptyplanets/downloads/Fix%20All%20Empty%20Planets%20v1.0.zip)
(didn't test with colonized empty planets, so use at your own responsibility if you colonized one)
Updated initial post.