The case seems pretty clear. If the the Prop 1A language doesn't allow bond money for Caltrain electrification use, then a new vote of the people is required to change the bond terms. The legislature cannot change how the money is used by itself. If this were allowed, the legislature could redirect this bond money to any cause it wants. The people's vote then means nothing more than approving a slush fund to be spent on the legislature's whim. That's why California has propositions. It's a check on the legislature to prevent bait and switch.

If the legislature thinks Prop 1A's intent is to fund these regional projects, then a judge will rule their interpretation is correct. No new legislation should be necessary.