The answer is....... Maybe!
Here's what I was told by a master certified Subaru mechanic that I worked with a few years back. The Subaru Select Monitor 3 Cannot see if you tuned you car and then returned to the stock tune before you bring it in for service. All it sees is if the Checksum (ECU) identifier is a stock value, which it will be if you unmarry a COBB AP, or reflash your stock map using ECU flash. Although the value might not be the same as it was originally, there is no database of original values to compare to so there is no way they can see a previous flash.
Now the tricky part...this is what they say they do on large warranty jobs if there is a question. They will send the ECU to a warranty claim engineer and the engineer can actually look at the ROM data and make a determination based on a timestamp that is placed any time the ECU is flashed, and possibly deny a claim based on that info. The SSM3 does not have this capability, it cannot read the time stamp and therefore cannot tell when the stock reflash was done. Hope this is a clear explanation based on a very reliable source who would give it to me straight. If anyone else has any input on this, feel free and I'll try to get some more answers.