Considering there'd been untold years of constant brain washing, retraining and wiping, Clint figured the break down would've started sooner, but apparently the perceived failure of protecting Jefferson triggered the beginning of it. Which was probably understandable, since Jefferson was potentially the first handler that Barnes had that wasn't a total douchenozzle.
"Yeah, Loki is the technician. They've got a slightly different system in place since your last... session." Clint wasn't entirely sure how the programming worked for HYDRA, the Red Room was nothing nice and he doubted HYDRA really cared about their agents comfort while wiping their brain to start again.
"Pretty sure it's okay to just," Clint's hand waved in the direction of where Barnes was sitting currently, figuring that Loki wouldn't need him to move, he'd said wherever was fine after all. "This is fine, right?"