Strange, that does not work for me in Eagle 9.6.2.
Almost 2 years later, I see the same issue as the original author of this question: After editing the 3D package of a component using the "EDIT3D" command, the device in the library does not contain the 3D package. I only see the grey box that is assigned by default to all devices, see screenshot of Library Editor's device view:
Library Editor, Device view
Clicking "Create new version..." in Library Editor does not change this.
I just noticed, however, that the "Inhaltsverzeichnis" (guess that's "Table of Contents") of Library Editor shows a new icon next to the device where I edited the 3D package:
Library Editor, overview
What does that mean? Could not find it in the manual.
When I double click on the icon, it disappears. And I get the notice that the library has been changed.
Now I can save the library and click on "Create new version..." and open the device again in Library Editor. Then I see my 3D package:
Library Editor, Device view with updated 3D package
Mind you, this workflow does not always succeed. I followed this workflow for another device and now the 3D package looks like a cog wheel:
Library Editor, Device View, cog wheel
This library management is baffling me.