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I'm fairly certain Magnetic Shield's redirect effect used to be applied earlier in the attack check, but that seems to have changed, possibly with the rework to Protect.

I know this is a very specific thing that only matters in certain fringe cases, but can it apply earlier on, before other effects (like Protect) kick in?

Protect doesn't apply in the attack check at all anymore, it applies well before it, just after the skill's target is confirmed.

So no, probably not.