CirCad.
End of 2009.
It's not an Ubuntu problem, it's a gEDA problem. One of the more friendly gurus hinted that fixing this issue would not be trivial. It is in general a pretty good software but IMHO not ready to be used in large and hardcore analog designs. You must be able to lock in multi-part device positions or in gEDA speak multi-slots. IOW the renumbering can rename U17A and U17B to U29A and U29B but not to U29A and U24B.