ChemDraw Beta 21.0 Portal
I actually use Chem3D!
It isnt obvious that you are doing any work on it? It's pretty buggy which is a shame because for a certain level user it could be very useful.
Example. Get the structure of cholesterol in the Chemdraw panel. In Chem3D minimise it, hide non polar H atoms and lone pairs. Picture 1.
Now, in the Chemdraw panel mouse over C-12 and hit 'o' to change it into an oxygen atom. The entire conformation changes. Why? Picture 2.
This makes it very hard to draw a structure, make a small change, and compare them
(oh, and in the time it has taken to write this, Chem3D has changed to a spinning ball, the only solution to which is terminate it and start again....
Chem3D opens a whole new world of visualisation during energy optimization, predicted spectra or calculated orbitals. It provides interfaces for 3d party computation programs (Gamess, Mopac, Gaussian). Love of this app grows up with experience of using it. I agree, that some GUI elements need to be aligned with current world of Win10, but to be fair, regular chemists are blessed with opportunity of smooth integration of drawing the structures in ChemDraw with a following 3D optimization in Chem3D. Due to mathematical complexity of such optimization and exponential time increase even for semi-empirical calculations of slightly bigger molecules, it doesn't allow wider adoption and love from everyone. But the developers are doing everything possible to open a door to the 3D world of organic chemistry wider for everyone:
No more awkward drawings in Chem3D, we have ChemDraw live link or a simple copy-paste from ChemDraw;
Tons of sample files with energy optimizations are provided (it would take ages to get those computations on a regular laptop).
As of your issue with substitution on Carbon to Oxygen atom in cholesterol, a simple editing at 3D window using "Build from text' tool from Building Toolbar is more elegant approach and doesn't unpredictably affect spacial coordinates of the rest of cholesterol structure (use Captial O, VD-CDBETA21-I-58.mp4).