yes you can with no harm done.
when you trim, you get sticky shears and fingers, you scrape it off the shears and rub it off your fingers, boom boom, hash
anything that puts sodium ions into the water is bad. your swapping out chlorine/chloramine ions for sodium. as i understand it, thats bad.
but i could be wrong, so wait for others advice
PERSONALY,k i would harvest. those brown leaves can cause some serious bud rot. i know from experiance.
its not allways noticeable from just looking.
but wait to see what others think, as i live in a damp climate
you could put the light closer to them, and a fan would build the strength on the stem. but as Dboybudz mentioned, put soil in to fill the cups up, pressing gently around the stem to firm the soil around them. eventualy they will develop roots all the way up the stem you cover with soil