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The problem with removing the Flex Fuel sensor on a car where it was tuned in, is if the diagnostics are enabled(and maybe even if they are not), you will get a CEL for FF sensor failure. Then the ECU will lock in on a default ethanol content as part of the failure strategy. I think the OEM value is 40% Ethanol. So if you pull the flex fuel sensor and put 93 octane in, the ECU will treat it like E40 and run super rich.
The tune needs to be removed. I would think most tuners would flash the stock file back in for free in your situation. At least I would.
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