When R7 astromech makes you re-roll attack die(s) do you still get to apply expertise (assuming you have already applied it to your first roll) to your re-roll?

You won't have applied it to your roll yet. Defender modifies attack dice first, then the attacker-- so there is no Expertise opportunity until after R7 triggers.

As Rampancy said ^^

But yes, rerolling dice does not prevent token/ability use to change certain results (such as focus) into other results (such as hits).

Your only limitation is that dice may only be rerolled once.