How much pad do you have left. If you aren't down to .5 mm on the pads and 1.5 mm on the rotor then you might try sanding them. Though you need to be sure those are the limits for your Shimano brakes. That's what they are for my brakes and rotor.
And use a block under the sandpaper so you don't start making a uneven surface. Not a 3m pad or something soft that will gouge out the softer parts and leave low and high places.
Otherwise get all new. And don't go crazy trying to bed them in whether it's the old ones you sanded or all new pads and rotor. Just firm braking and not to a complete stop. I didn't bed mine in at all. I just did normal braking and 300 miles later they were very effective at braking and no noises except for briefly in wet conditions.
And be certain the rubber boot around the pucks are clean and no oil seeping out. A tiny drop of oil every few 100 miles might be your issue too. A q-tip or swab will let you get up in there.