Connect 2 BGA pins before soldering IC?
PCBs are cheap nowadays. If you haven't yet assembled (you say bare boards), its probably easier to just respin them.

Failing that, if this is for a one-off, and given its a reasonably large pitch BGA, you could try something like the following:

Scrape some of the soldermask off the via - say the half of it closest to the two pads that will end up connected. Basically try to keep away from the two pads below which you don't want to risk shorting out to.

Onto the via, solder some very thin bare copper wire (e.g. one strand from a multi-stranded wire). Make sure the solder is not too thick that it interferes with the height clearance of the BGA when placed.
If possible, try to place some of the wire down into the via, as that will help anchor it and stop the surface tension of the reflowing solder from pulling it off the via.

Cut the piece of soldered bare wire and position it such that it is just long enough to cross to the far side of the unconnected pad. Don't solder it to the pad, as that would cause excess height on the pad when reflowing the BGA.

Apply solder paste to the pads. This should give enough stickyness to hold the piece of wire in place.

Reflow the BGA.

Hope!


With a bit of look the piece of wire will bond into the reflowed solder balls on the BGA making a decent stable connection. As long as you are careful when placing the BGA not to slide it around, it should cause no problems soldering.