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So Jain Zar's mask does -5 to initiative down to a minimum of 1 when she's within 6 inches of a model. Then a warp side shoots using monofilament which resolves vs. initiative not toughness. Can I combine these two skills?

I don't see why not. The mask modifies the profile, so the new value is used to wound.

Provided the modified Initiative is that of the unit, or the unit's majority Initiative, sure.