Two reasons.
First, it's possible that the conversion could be less "remove beam, pour concrete into beam until flat" and more "remove beam, remove entire bridge section, fabricate and place new bridge section." There are different alternatives, and they haven't decided which to go with. Now that they know they have the money, they might decide to just go for the most elaborate option, with the only limitation being to not spend the money meant for the other stuff.
Speaking of other stuff, the conversation cost isn't just the construction. It's also building all of the associated infrastructure. Refurbishing the stations (Have you seen the Rosa Parks station concept from the TOD study? It's pretty dramatic), overhauling any and all related cabling (adding fiber), replacing signaling systems, probably a massive overhaul of the maintenance and operations center, redoing the payment system, and likely a bunch of other things related to the AVs that we're not aware of.