i would take them out of the pots. they could probably stay in, but i think as the roots grow, they would be restricted. to make up for not having the fertilizer in the pots, their are liquid fertilizers u can use that easily replace it. you might not even need this, but the biggest cause of browning plants (besides light deprivation) is iron deficiency. i use a product Hagans iron enriched plant grow, you just add a capful to every 10 gallons of water. its about 5 bucks a bottle, but it treats 470 gallons, so its pretty cheap. hope this helps
also, for most low light plants, you need close to 1 WPG (watt per gallon), although u probably knew this. what kind of lighting do u have?