The most reliable mention of wild brook trout in Cedar Run was published in the 1957 edition of The Fishes of Ohio, by Milton B. Trautman, Professor Emeritus of zoology at The Ohio State University. In his chapter on Brook Trout (pages 226-227 of the revised edition,1981) Dr. Trautman has this to say:

Trautman's book is not only the definitive work on all fish species (native and introduced) in Ohio, it is also an excellent primer on the natural history of the state. (from The Ohio State University Press, ISBN 0-8142-0213-6)		  
" In 1927 I found brook trouts propagating naturally in Cedar Run of Champaign and Clark counties, and the older residents of the vicinity informed me that this species had been present in Cedar Run for many years. Possibly these trouts were descendants of the 1882 plantings."

Why did Trautman theorize that the brook trout in Cedar Run were descendents of an introduced stock and not indigenous? Likely because there are no other documented instances of indigenous trout anywhere in the post-glacial (i.e. post Teays) Ohio River valley. In fact, the only indigenous brook trout in Ohio are a handful of remnant populations in a few tiny spring creeks in the Lake Erie drainage. These trout were identified as indigenous only recently via DNA testing (which of course wasn't available in 1927.)
Other references to "native" brook trout in Cedar Run, such as those by the Cedar Bog Association appear to use the word "native" to mean "naturally propagated" rather than indigenous. In common fly fishing parlance, though, a "native trout" means one indigenous to the stream, but a "wild trout" means one born in the stream– regardless of the origin of its ancestors. Thus Cedar Run might have "wild" browns and rainbows, but neither can be "native", since both these species were introduced to Ohio (browns from Europe and rainbows from the western U.S.)

The state of Ohio has stocked the Mad River system for decades. Some of these trout mature in the wild and attempt to reproduce. Those that find their way to Cedar Run are probably successful. In the early 1980's the state DNR in cooperation with local chapters of Trout Unlimited and the Federation of Fly Fishers, attempted to incubate brown trout eggs in the Mad River and several tributaries. Only those eggs placed in Cedar Run had a viable hatch rate. This no doubt was due to the superior clarity of Cedar Run, since silt appeared to have smothered the eggs in the other incubation sites.

So if you catch a trout in Cedar Run, is it wild? That would be difficult say. Technically "wild" means hatched in the stream. Since any trout hatched in Cedar Run is likely descended from a hatchery raised trout, there wouldn't be any significant genetic differences between it and a trout straight from the same hatchery as its ancestors. Obvious signs that a fish was raised in a hatchery would be misshapen or missing fins and overall drab colors. However, a trout released into the wild at a young age is virtually indistinguishable from wild trout from the same lineage. So just because a fish has perfect fins and vibrant color doesn't mean it was born in the stream. At the moment, no one knows for sure how many of our trout are wild. Through our restoration effort we are increasing the number of wild trout in Cedar Run. Rest assured, as time goes by, more and more of our trout population will be wild.