When changing from a ligand puzzle to a non-ligand puzzle, the "Small-Molecule Design", "Small Molecule View Options", and "Small Molecule Properties" windows remain open.
The "Small Molecule Properties" menu even reports items like molecular weight and polar surface area on non-ligand puzzles like the June 2022 Design of the Month. (The values reported seem a little lite.)
The "Small Molecule View Options" also provides isosurface and other visualizations. In the June 2022 DOTM, these visualizations cover only part of the binder protein.
The "Small-Molecule Design" window even comes back after a restart. It will survive multiple restarts.
The other small molecule windows (view options and properties) are cleared by a restart.
All the ligand-related windows should close if the current puzzle doesn't have a ligand.