Only immune to attacks relying on genetics. You can still kill it with fire, nukes or drain-o. And if you genetically engineer a counter-attacking virus to go for the newly engineered cockroaches, it can't spread into the main ecosystem, it can only attack other organisms with the "new" alphabet. And if it did go tits-up, then screw that ecosystem and start again with another alphabet!

In Greg Egan's "The Moat", this is exactly what a group of people do - breed a new race of humans using non-standard base pairs, thereby meaning that they cannot interbreed with anyone, just the "genetically superior" members of their own race: and rendering them immune to all viruses and preventing imperfection creeping in from quick forays into the bushes with the "inferior" milkman.

I doubt we'd find viruses adapted to the new chemistry very fast. Finding a way to metabolise a new chemical (eg E. coli and citric acid) is a long long way from being able to totally replace all the base pairs in an offspring in one go. The way I understand it, a half-formed mutation (eg replacing only two of four bases) would be line-ending, as the offspring could then not infect any cell, normal or "new". It's not impossible, but it would presumably take a long time to make that jump, perhaps by some more roundabout way, like a dual-stack approach. So, IPv6 vs IPv4 in biological terms then.