If Louis II would leave only daughters, then most likely a husband of one of these daughters (usually the eldest) would 'inherit' Bohemia and Hungary (& Croatia) in her right, or rather he'd be the one elected in her stead (but his legitimacy comes from his wife).
Perhaps the Bohemian and Hungarian Estates choose the husband from a different daughter though.
OTOH given the Ottoman threat, especially Hungary still needs support from the Austrian Habsburgs and Poland-Lithuania, which will be inclined to do so (maybe after some concessions) since otherwise they will (or at least might) be next.
So something like what Ferdinand did, except instead of claiming the inheritance of Louis' sister, it would be Louis' daughter.
Anyway, I thought Bohemia was under Salic law?
I didn't feel like creating a new thread, so I'll ask it here: WI Louis still dies in 1506 fighting against the Ottomans, but is survived by daughters with Mary of Austria? Considering the couples age, any daughter of them wouldn't be elder than 5 years old by then, and so she wouldn't be married (although Louis and Mary were married being only 9 and 10, respectively). Let's assume his daughter isn't married yet then. What would happen to the sucession? Would the Bohemian and the Hungarian nobles accept an underage girl as their monarch?
Someone I'm very curious about but I can't seem to find any further info about it, is Janos Wass (Lajos' illegitimate son). I wonder if Lajos' legitimate daughters would've inherited Janos' ridiculous fertility (he supposedly had 12/14 kids)
What about her marrying her cousin in Poland? To make a sort of bulwark against what might be seen as the Habsburgs getting too powerful? Of course, this might hinge on Sigismund the Old having more than one son, but if the PoD is at Mohacs, it's not impossible that either one of Bona's pregnancies is a boy instead of a girl or that she doesn't go hunting the day she miscarried her second son.