This will mostly affect the road bikes, possibly other brands, but I would guess that any KTM that takes a fuel map could be affected.
What have I found out? Well, in the true fashion of male, I found out the hard way. Getting your KTM tuned with Tuneboy can cause you issues with the original KTM equipment. Tuneboy works in such a way that changes to the ECU via normal KTM equipment will be over-ridden by Tuneboy.
Long story short, several services ago, a map from KTM didn't get my 990SM running just right, but the shop had done what it could with what it had available. Rather than a piggy back I didn't really have space for (ie, a PCIII - which wasn't available at the time), I opted for the Tuneboy method.
Had a first tune, somewhat improved, but not there yet. Fast forward to last week, bike goes in for another service, and the workshop can't figure out why, when they run the bike through diagnostics the map has changed and the bike is ignoring some of the changes they make. New software is available, and a new map too, which can't be used.
The major issue for me? I can travel a lot, and if I ran into issues say, in the South Island, a KTM dealer down there wouldn't have much success with the bike, even getting my data sent down from Auckland.
So just be aware that Tuneboy could restrict how much your shop could work with the bike. Once the bike is in one piece again, I'll arrange to have the stuff removed, so the shop can work with the new map etc.
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