The actress, 47, alarmed viewers when she was absent from Tuesday night's elimination episode, but Chmerkovskiy, 32, says she's just taking it easy at home.
"She's in pain," he told PEOPLE backstage after the show. "She's got a big headache. The doctors said she has a minor concussion, and I know that's really unpleasant."
Chmerkovskiy is optimistic that Gilbert's setback is only temporary and won't keep them out of the competition.
"I think we are coming back," he says. "I'm pretty sure. It's not up to me, it's up to her, [but] I haven't heard talks of not coming back. Although, if she wakes up tomorrow and continues to have a headache, I won't let her in the studio."
The week's events do have the dance pro reevaluating his ballroom tactics, questioning if it's worth it to put so much effort into the dances and risk injuries, only to be eliminated so quickly like favorite Sherri Shepherd, who got the boot on Tuesday.
"We owe it to our fans to give them a reason to vote for us," he says. "I've always been very vocal about how you have to earn your stripes. But I'm not sure if this is the right strategy this season, because it's clearly not appreciated."
Even though Chmerkovskiy has "a problem with easy choreography," he says, "Honestly, at this point, I'm not really sure if it's worth killing yourself and trying to put on a show."