Frame Challenge: It doesn't matter whether you reroll the damage dice, you can't make the spell leap
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. Conceptually, it takes what was one die representing three different things and separates it into different dice, all reading the same roll. Then it lets you reroll the die representing damage, but not the 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.
SupportIndirect 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. Overchannel does not let you reroll the dice of Chaos Bolt, but rather sets damage to the maximum. In doing so, however, GreySage argues that changing the damage aspect of the dice does not alter their other aspects - just because the damage is now 22 (8+8+6), does not make the Chaos Bolt leaping thunder damage. While not directly analogous to the situation with Empowered Spell's actual rerolls of physical dice, I believe its distinction of the different functions of the dice (damage amount, damage type, ability to leap), supports this answer's interpretation of the question at hand.