I think he'll come around but it may take weeks, months. When I was moving my pleco once, he got caught in the net and I had to fiddle with it to get him out. He used to be very friendly with me, coming to my hand to eat and after that he became terrified and hid when he saw me. It took him several months to come around but besides that, he was not showing other signs of stress. Bagging the fish may have exposed him to gill ammonia burn and it is not always recoverable but for an hour or so only, hopefully that's not the case and he just hates you right now 
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