Once we're sure the patents have expired would it be ok to clone the chips? All the parts are getting old and we will be needing replacements.
What do you mean by "cloned".
There is nothing inherent in the patent system that prevents you cloning a chip as a patent only covers how the design works. Patenting a chip doesn't stop someone from producing something that is pin compatible, it just has to work in a different way (depending on what is patented the chip could have seemingly identical characteristics).
If you actually want to make a copy of the chip by photographing the original mask, then that isn't a patent issue but a mask rights issue.
http://en.wikipedia.org/wiki/Integrated_circuit_layout_design_protection copyright doesn't cover masks because there is no artistic merit to them, but since 1989 you do get rights for up to 15 years to prevent people making copies.
The CPU in the NES was produced prior to this coming in and the chip was cloned by NEC(?) de-capping the 6502 and photographing it and then cutting out the bits that were patented (like decimal mode).
It seems strange that this type of practice went on. A lot of chips were produced by multiple companies as second sources, because some manufacturers wouldn't buy a chip that was only produced by one company, as they could end up with supply problems. I don't know whether they just had to pay to license the patents.