I know your pain. I've been thinking about this myself. I would like to think I've got a pretty good relationship with my dealer. I think in this case, honesty will be my best policy. When I take it in, I will tell them that I think all it needs is the fan relay (I don't remember at the moment whether or not the fan stays on - IIRC I think it doesn't). IF they diagnose it to need an ECU as well, I want them to let me know BEFORE they pull it. I will tell them that I am not running a stock map and I need to 'reset things' before they replace it. And that I will need to put my map back before I can take it home.
I think I can get away with it because:
- I'm being upfront and honest with them.
- I bring my car in for service there. For everything including oil changes. Quite frankly, you'd have to be asleep at the wheel to not notice 'things have been done to my car' when you put it up in the air to change the oil. Cobb UP/DP, a 2x sized intercooler, pink springs and blue sway bars are kinda hard to miss. Not to mention the 1" drop in ride height. Should be instantly noticable to someone who gets in and out of Subarus all day long.
- At 48k miles, well, I'm past the warranty period anyway.
- In the 4 years I've owned Subarus (my second Subaru, all of them bought/serviced there), I have never made a warranty claim.
Then again, I guess we shall see!