Not that anyone can blame the department for wanting a new CSI investigator with Barry M.I.A. for so long and Julian Albert reportedly out for Season 4.
Still, the fact that Joe is stressed and upset about Barry potentially losing his job shows his worry towards affecting Barry’s future, and whether or not he will ever see him again is pretty deep.
For Joe, it sounds things are extra hard compared to the rest of the team, as Jesse L. Martin explains he and Iris have to cover for Barry’s absence from the CCPD, which is on the verge of giving his job away.