>>From what I understand, the main problems are happening when destroying
 > and recreating the window arragnment.  How about adding a function that
 > toggles or changes the window arrangment non recursivly, which will deal
 > with all the backend details, and the main rotate function can just
 > recursivly call that on all windows.

I attach a function 'resurrect-window' that rotate/transpose/flip
functions can call to resurrect the previous windows after having
deleted them.  Tested with:

(let ((dead (split-window nil nil t)))
   (set-window-buffer dead "*Messages*")
   (message "%s" (next-window))
   (sit-for 2)
   (delete-window dead)
   (let ((live (split-window)))
     (resurrect-window dead live)
     (message "%s" (next-window))))

martin