They use EDA (Electronic Design Automation) software, there are only a handful of vendors, the largest probably being Mentor Graphics, now owned by Siemens. So, yes, they use automation to algorithmically build and track/resolve refactors as they design CPUs. CPUs are /generally/ block-type designs these days, so particular functions get repeated identically in different places and can be somewhat abstracted away in your EDA.

It's still enormously complex, and way more complex than the last time I touched this stuff more than 15 years ago.