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Did Yenko remove the "396" fender tag and put in his own 427 badge in the same holes?
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That's a darn good question Marc, and to tell you the truth I don't think anyone has a definitive answer to that. The '69 Yenko S/C 427 Novas are unique in the '69 Yenko lineup in that they were not COPO'd factory installed 427s like the Camaros and Chevelles, but were instead converted from RPO L-78 SS396 cars very similar to many of the Yenko 427 Camaros in '68. Being that they were SS396 cars to begin with, looking very much like
this (with the possible exception of the brightwork around the windows and rockers) they all would have received the cast front fender marker light bezels with "396" engine identification from the factory.
While it isn't completely known for sure how Yenko then rebadged these cars as 427s, it seems there were at least 2 different practices used. The stock 396 bezels were sometimes removed, and replaced with smaller, plain bezels with no engine size, as used on 6 cylinder Novas in 68-9. Then Yenko's crew would add their own 427 emblems ahead of the bezels, doing their best to cover/utilize the extra hole where the original 396 marker bezel had been factory installed. This method required the installation of 2 new parts per side, a new plain marker light bezel and Yenko's own designed 427 badge.
The other method of correcting the "396" marker light bezel problem, was to simply remove and replace the "396" bezel with a cast GM "427" marker light bezel as used on big Chevrolets in '68. The latter made for a cleaner, neater, more factory like appearance, but may have been more expensive, so Yenko may have favored the use of his own 427 emblems more often. This is only speculation on my part.
Being that so few of the '69 427 Yenko Novas exist today, and most lived very hard lives and were subject to lots of abuse and modification over the years, there is little to go on in terms of unmolested surviving examples to give us the definitive answer we're looking for. Not to mention that each car was hand converted and things like emblem and stripe placement variations abound in Yenko's "process" for converting supercars.
To add to this mystery, I know of only one surviving period photograph of a '69 Yenko 427 Nova, and unfortunately it is a rear shot of the car on a carrier and the fender emblem placement cannot be determined.
I guess these "unknowns" only add to the mystique of these incredibly rare supercars. Maybe someday we'll luck out and an unmolested, "undiscovered" car will surface. Until then, I hope at least some of my explanation is helpful.