Your tuner should still work even if the PCM is reflashed.
From some conversations I have had with Jody at DP-Tuner, it is the "Family" number (the DPC-) of PCM that is more important than the actual PCM "code". The PCM "code" is sort of the version of factory-tune that is installed in the PCM. The "family" (or model number, if you will) of the PCM does not necessarily change with a different "code" (or tune). Does that make sense?
Again, your PCM's "family" number (DPC number) will be the same, only the factory tune (code number) will change with a reflash. And since the tuner's programming basically overrides the factory (PCM) programming anyway, you should be fine.
Here's a pic of the different numbers:
I used to have a list of DPC numbers and all of the "code" numbers for each, but I can't seem to find it. If I do, I will post it up.
If your chip was installed when the dealer did the re-flash, that may have damaged the chip...not good!
If the chip was
not installed when they did the flash, and you re-installed it afterwards, then I would suggest you go back and double-check the edge-card connection where the chip plugs in the the PCM. Make sure the connector is clean and the chip is fully seated on the connector. That is the most common cause for a chip to stop working.
Good luck. Let us know what you find...