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It is unlikely a dealer tech would be able to tell if an ECU/TCU tune had been removed if write counters have been reset properly. If there is a major problem, though, the ECU/TCU Is likely to be sent back to the manufacturing plant for fault analysis, at that point bench data extracted that may not be accessible via an OBD port flash would likely show changes from the original manufactured state. I would be surprised if there isn’t out-of-band (i.e. not in the remote flashable EEPROM) count and checksum information and in some cases time related information in any modern ECU, if not just to protect system integrity as opposed to tampering detection.
Although my manufacturing fault analysis goes back to mid-frame disk drives in the late 80s, even then we could obtain a lot of change data from the device from bench analysis in our lab and manufacturing plant, that could not be accessed via the drive’s interface.
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