The dealer can't tell that your ECU was flashed. They don't have the hardware nor do they have the "brains" in the shops. To tell if the ECU has been altered, they're sending your ECU away.
The Woolich stuff works transparently with the KDS tools at the dealer. My 2011 has been flashed since god knows when and been through two recalls and I just recently re-extended the warranty last June. My 2016, has been flashed since the day I got it, almost a year ago to the day. It has been through one recall, still got my factory and extended warranty. You have zero worries about it. If you're freaking out about it and you have the proper software, you can reset your ECU to stock before bringing it in and then when done, reflash it to what you had on there before after you get the bike back home. Takes all of 2 minutes to do.
But your issue is most definitely tune related. If you have zero idea what you're doing, best to bring it to someone and have them tune it for you. Also, depending on your location, there may be things inside the ECU holding it back so you may want to look into flashing the ECU and if you find the right shop, they will have the hardware there to do it all in house without any extra added hardware on your bike.