In my mentioned first attempt copying AE into a 2nd folder, I made the mistake to a) create a directory manually - and b) then copy only the content off the stock AE install into that new directory.
The 2nd attempt, I copied the whole install directory (clicking on the directory itself to copy it), then renamed it replacing the suffix Admiral's Edition with Babe's Edition - and it worked.
The only TARGET or START IN pointer I had manually to change was the Editor's one (i.e. where to look for the scen files to open).
I use Jonesoft's mod swapping tool too, but I strictly want stock and Babes separated, as two completely independent installs. There's just so much difference (different slots of units, means different unit patches slots, pwhexe, map and whatever) that having it all in just one install is not the way to go for me - and this way I can play stock AND Babes at the same time without swapping anything around.
"A big butcher's bill is not necessarily evidence of good tactics"
- Wavell's reply to Churchill, after the latter complained about faint-heartedness, as he discovered that British casualties in the evacuation from Somaliland had been only 260 men.