The actor had a back injury on set. They could not write him out for the first couple of episodes hence him always sitting. He will not be in a couple of new episodes but will return later in the season.

Yeah I think he'll be back for the 100th ep this season, even if its just a cameo.

From the 10-31-18 story on TVLine:

"My husband and I watch The Flash and we’ve noticed that Jesse L. Martin has been sitting down in all of his scenes. Are we crazy or is he injured? –Rachel No, you are not crazy but perceptive – though this week we did see Joe leaning in a doorway at the CCPD. I’m hearing that Martin suffered a back injury over the hiatus. In fact, a studio rep confirms for TVLine that the actor will be taking a medical leave from the CW hit, adding: “We wish him a full and speedy recovery and look forward to his return as Detective Joe West.” (It’s unclear at this time exactly when and for how long Joe’s absence will be felt on screen, but sources tell me it will be addressed at some point.)"

There are other stories from other sites but they all say basically the same thing: He is taking a medical leave at this time with no time of return stated.

I hope he's okay, "Back injury" is sometimes used when they have something degenerative I remember back in the 90's when Michael J Fox claimed back injury, before he publicly revealed he had Parkinsons, likewise Meatloaf clearly has something similar but claims he's had a bad back.