A second possible answer, and one that is more in line with my current thinking, is that the d8's used are serving many functions. They are damage dice, to be sure, but they are also determining what kind of damage the spell does and whether or not it leaps to another target.
Empowered Magic lets you reroll the damage aspect of a die or dice, but does not alter their original value for their other aspects. This interpretation does not address your specific question about whether the dice may be rolled sequentially, but it makes the question itself moot if your goal was not to change the damage rolls but to try to generate a leap.
Support for this interpretation can be found at How does an Evocation wizard's Overchannel feature interact with the Chaos Bolt spell? with both GreySage's well-received answer and Xirema's as well.