Haste makes waste, as the saying goes. In 2008 the Chatsworth crash happened and led Congress to mandate the installation of PTC signaling systems on every railroad in the US by 2015. They gave railroads 7 years to do a huge nationwide rollout, in a country where even minor changes to our infrastructure can take 15-20 years. Congress also gave no funds to railroads to meet this deadline.
Because of the tight timeline and lack of funding, Caltrain chose a system called CBOSS that was kind of a hack, an overlay of additional functionality onto their existing signal system rather than a whole new signal system from the ground up. They knew in theory that HSR may be coming to their tracks, but the deadline from Congress meant they couldn't wait around for 5 or 10 years while CHSRA figured out the tech standards for their new rail system. There was also a chance that HSR would build a new alignment on the Peninsula and wouldn't need to share tracks with Caltrain at all.
Of course, eventually CHSRA caved to NIMBYs on the Peninsula and agreed to a blended system, meaning that Caltrain's CBOSS wouldn't be compatible. They decided to use a system called I-ETMS, which has become the PTC standard for US rail mainlines. But that was after sinking $200M into the failed CBOSS. Other issues arose too, like the fact that CBOSS contractors laid fiber optic cable right in the path of certain foundations for the overhead catenary system. The whole thing has now gotten tied up in a predictable but very messy/complex lawsuit.
You can read even more technical detail at Clem Tillier's blog:
https://caltrain-hsr.blogspot.com/se...0&by-date=true