Multiple Ground Planes
Yes, tie them together. Do NOT leave any floating copper since it can form an unintentional patch antenna. Note that grounded copper on the trace layer may lower the trace impedance slightly.

You should add plenty of stitch vias to make sure the copper islands on trace layer are grounded to the plane with low impedance at 400 MHz (that frequency was chosen because you mentioned it in your question). Any islands which cannot be stitched to the main GND plane with vias should be milled out altogether or removed with hand tools.