I believe the theater is currently being used as a preview for Tomorrowland. Once that is done, there has been speculation that it will be Captain EO again, but no confirmation
DisneylandToday confirmed on Twitter that the theater "will reopen mid-July with a to-be-named attraction." As thmcdonald1 mentioned, the rumor is that it will be a Captain EO return.
I'm crossing my fingers, as I'll be there for my birthday in September, and my one birthday wish I told the CM when we booked our package was for a Captain EO return.
I do NOT expect it to return to Captian EO. I expect it to be continued to be used as a preview center the next Disney/Marvel/Star Wars movie, until they decide to put a permanent attraction in its place.