Your replenishment water doesn't need much in the way of a pH adjustment, unless it's out of wack. Evaporated water leaves the buffer in tact so that add-back water is stabilized. That is. . .unless the add-back water is really off track. Is the filter water pure enough? Have you ever checked it for ammonia, nitrites, phosphates, silica, organics, and other things? You might consider switching to DI or distilled water for replenishment.
Stress doesn't mean that you are the one doing it. A fish responds to stress in minutes, hours, days, or even weeks. So, it doesn't have to be a stress from you. If you can see any damage to a fish, trust me, that could be just the tip of the iceberg. It's what you don't see that will bite you. I suggest you read this short thread for some insights:
http://www.reefcentral.com/forums/showthread.php?s=&threadid=800280
Don't hesitate to refuse a fish that you think was hurt during its capture. You might say to your LFS that you will buy that fish, but until you've paid for it, it is still theirs! So if for any reason you don't like the looks of the fish when it is in the bag, after capture, tell them you don't want it now.
I think it'll be okay if you give it rest, good foods, TLC, and some treatment. :rollface: