When you play Moonfall on a battlefield where you have units, and your opponent plays Flurry of Blades in response, will Moonfall still fully resolve and apply its effects even if all your units at that battlefield die before Moonfall resolves?

Yes — Moonfall will still fully resolve and apply its effects.

Moonfall targets a battlefield, not your units. The phrase "where you have units" is a targeting restriction for choosing which battlefield you select when you play the spell (Rule 355.10.b) — it is not a separately targeted game object. When "Flurry of Blades" kills all your units at that battlefield before Moonfall resolves, the battlefield itself remains a legal target (battlefields can't be Killed, Rule 170.3), so the spell resolves normally. Per Rule 359.3.e.6, instructions that can still be followed are executed as much as possible.

There's one nuance on the move effect: if the enemy unit you chose to move was at that battlefield and has since died to Flurry of Blades, the "move up to one enemy unit" instruction will be ignored since that unit is gone (Rule 359.3.e.7). But the -2 Might effect is independent — it applies to whatever enemy units are at that battlefield when Moonfall resolves, even if they were the ones who just survived Flurry of Blades themselves. If Flurry killed both sides' units there, the -2 still applies to any enemy units that were moved there by another effect or remain alive at resolution — and it will snapshot at that moment, affecting only enemy units present then.