These funds were a terrible idea in the first place. It took years and years (and years) of politicking to get the HSR bonds placed on the ballot. Supposedly the planners for HSR had to agree to a $1 billion payoff to all of the existing state rail systems in order to buy their silence, so of the $10 billion for the bonds, only $9 billion even goes to HSR at all, the other $1 billion is to be spread out about 8 other agencies such as Muni, BART, etc. based on a formula that compares each agency's size/ridership. The money was described as being for "connectivity" but there were not rules describing what that meant so it was basically a slush fund for each agency to apply to their pet projects and they didn't have to have anything to do with HSR up until Jerry took office.
So all of these other transit systems are blatantly skimming off of the top of the HSR bonds and some of the projects they want to spend the money on are exactly what you would expect - projects that would not get voter approval in their own right, so they use money that was sold to voters as being for one thing and then re-route it to something unpopular like a light rail line that is all of ~1.5 miles long at best with a whopping four stations that still clocks in at $1.6 billion with costs still rising.
Worst of all, it's not like the HSR line is all paid for either - even with strong future federal assistance, the state and local governments will have to come up with more money down the road if HSR is ever going to be completed as envisioned, so giving away $1 billion of bond money now, that will be financed and cost the state closer to $2 billion over 30 years, is pretty ridiculous - and sooner or later people are going to get wise to it and that will only hurt HSR and voter confidence in any large infrastructure project so it's shooting yourself in the foot. Sometimes it seems like Jerry is the only adult in the room.