I recommend that you remove them. You should have at least 2.5 to 3 inches of gravel. Many plant keepers have 4 inches of gravel.
Having potted plants in a tank is not visually appealing, but if you have uprooters (ex. Cichlids), then you'll probably need to keep the plants potted. I had Clowns (Botia) that constantly uprooted my plants. But they also ate it, so keeping them potted would have been a waste of time anyway.
Lissette