Looks like all you need is a file called version in the root of your frameworks/cocos2d-x-3.9 folder with the version pasted in it.
Example contents of version file: cocos2d-x-3.9
Edit:
Also, I needed to do the following:
- Copy
templatesandtoolsfolders from a previous install ofCocos With Frameworkinto the same location in Cocos Without Framework. Note: NOT thetemplatesandtoolsfolders inside theframework/cocos2d-x - manually set paths in
tools/cocos-console/bin/cocos2d.ini