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I had the exact same thing happen to me with my 2002 F350. It did wind up having a stock file in it, but for some reason the Edge Evo CS I was using would not recognize it as such. Be warned: Dealer reflash DID NOT solve my issue. (for $95 too!) Edge sent me a stock writer, then remotely reset my Evo to do it's thing (for FREE!).
Don't take the programmer's 'word' that your truck is tuned. I think my issue is that I did a Bully Dog "try before you buy" and it left a 'footprint' of sorts that the aftermarket programmer flagged as non stock programming. Either way you still have an issue as the new programmer won't continue without seeing the stock files. Call SuperChips tech support, they probably have seen this before and will know what to do. I got very familiar with Edge's Tech (Thanks, Jordan) while they worked to get my issue resolved.
2002 F350 XLT CC LWB PSD 4X4 AUTO, 6637 w/Pete's cover, MBRP 4" T-409 Turboback, Edge Evo CS, AutoPage Remote Start/Keyless, and a decent stereo.