If your peppers appeared healthy and turgid prior to thinning and soon after thinning they went limp I would lean towards overly aggressive thinning. I used to be a "plant plucker" thinner, but would end up losing some of the seedlings that were left behind. After identifying the plucking to be an issue I have turned to clipping with scissors to thin.
You did say you were over exuberant, how many seedlings per hole or square inch did you end up with? Also about how old were your pepper seedlings when you thinned them out? The older the seedlings are the more lateral roots that would be put out and then be damaged by plucking the peppers out to thin them.
http://www.soilandhealth.org/01aglibr...
I found this near the bottom of the linked page just below the summary
"Root Habits in Relation to Cultural Practice.--Much of what has been said about the preparation of soil, transplanting, and cultivation of the tomato applies also to the pepper. Where the seed is sown in hills in the field great care should be exercised in thinning, especially if the seedlings are thick, so as to disturb as little as possible the roots of the plants left. When possible, irrigation is advised after thinning to prevent wilting."
I personally would treat your seedlings nicely giving them a humid environment cover them with a cup or something to reduce transpiration stress, maybe even reduce the light they receive Give the surviving seedlings roots time to reestablish.
Please add a comment back if your plants make it out okay.
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