I removed TRR, no change.
I just uninstalled Kopernicus & KopernicusExpansion along with JNSQ and some mods related to it (JNSQ Kerbinside+JNSQ Visuals). Surprisingly there's no problem! I can close the warning message and create a new save.
I also did a manual reinstall of Tweakscale and MechJeb2 because Tweakscale showed a warning.
Definitely Kopernicus related. So what now? I can't just switch to stock planets, what about my save?!
And as for your question, I did update Kopernicus to the latest version (224) using CKAN.