Disconnecting the battery does not wipe any info or memory it only restarts the cycle,
and while you can reset some of the error codes they still stay in memory even though you pulled the battery.
Flashing the PCM with a Tune wipes the memory, well it's suppose too anyway.
To clear codes you need to hook up a scan tool and not all scanners can completely erase them.
I never did the SCT Tuner route, so I do not have the personal experience that you have.
But I do hook up my Actron recording/scanner tool and data log to Whipple.
I'm just quoting what was told to me and I'm just trying to help with some info from reliable sources.
I waited till Whipple was done with testing in the spring of 2011 which gave me 3000 miles to brake her in nice.