That question, maybe surprisingly enough, makes Inigo go quiet for a moment. His movements slow down too until he just stills. Apparently it's more impactful than Prompto meant it to be - or Inigo just has to think about it for a moment, just has to really let that question dawn upon him, like it's something he hasn't thought about very much yet.

".. yes," he then answers. Inigo smiles softly. "I've really missed her."

Both here in this place, but also back in his own future, where she's been dead for so long. Thank god the former meaning being obvious means he doesn't have to reveal the latter.