Lewis was stretchered off in some discomfort with an ankle injury in the first half and his replacement Miller - who scored the Gills' second goal - then limped off with a foot problem.
Dennis Oli and youth-team star Luke Rooney were also on target, but manager Mark Stimson was concerned about the well-being of two of his key men.
"They're not in a good way to be honest," he said. "They've gone to hospital to see if we can find out any information on what they've done but I'd be surprised if we can get much detail because they are both very swollen in the area of their injuries.
"On Saturday (at Welling) I wasn't too happy because of the result but I realised when I got home that results don't mean a thing because the massive plus was that we didn't get any injuries.
"Here we've won the game but picked up two injuries and that's a nightmare. We'll probably have to wait a week to find out how long they're going to be out."