Flandre has the power to destroy ANYTHING and everything. An immortal is still a "thing" so is included in the "anything" realm, i guess. Flandre herself is immortal, but (despite a few references to suicide) probably doesn't want to destroy herself despite having such a hard life. So, who knows.
Remi, Flan, Kaguya, Eirin, Chang'e and Fuijiwara (AKA Mokou, but i prefer her surname) are all immortal, and possibly that vampire gateguard from TH4, that i keep forgetting the name of. Unless they are a vampire, they obtained this from the "Hourai Elixir" which states:
"Complete destruction results in complete restoration." - ZUN
so, due to this, if immortal via the Hourai Elixir, which most touhou immortal are, yes they can be destroyed by Flandre, but will be instantly reparied. " - Rumia, captain of the Seirensen Vanguard