I highly recommend you don't try this. Integrating two very different platforms is unlikely to go well or be a productive use of your time. You could potentially look at common CN changes identified by each, but trying to integrate them both into a single analysis is best avoided.

edit: OP also received an answer to this in the bioconductor slack regarding the originally mentioned CGH arrays, to which Henrik Bengtsson said you can actually normalize between platforms used for the same samples in a fairly robust manner with the aroma.cn R package, so TIL.