If I understand well, the 1929 version is in very good shape. What I never really understood, were the 1925 segments used for this 1929 version (excluding the newly shot scenes) lifted from the 1925 print, or alternate shots of the same sequences? in the first case, it must be possible to reconstruct the 1925 version, using all the shots lifted from the earlier one, and completing the missing scenes with the 16mm print. Of course, it wouldn't be perfect, but it's the method they used for the restored METROPOLIS, in fact.
If the 1925 shots in the 1929 version are alternate shots (but filmed in 1925), well, it would be slightly different from the original, but not so far, I suppose...
In both case, the final result would be probably better than the 16mm print, even in using some of its scenes.