Several days ago the red lightning bolt showed up for the second time in 2 days. I had already read the dire warnings in the manual and since I was only about 4 miles from home in a snow storm I turned around and headed for home. I never made it. Within several minutes more lights started to come on, the radio dropped out and the engine stumbled before stalling out. I couldn't even get it to turn over, completely dead. So I had it towed to the dealer. Eventually they called and said the battery was completely dead and the alternator had no output and needed to be replaced. This seemed strange since the car started easily less than 10 minutes before appearing completely dead.

So anyway after dropping $500 the car seemed to be fixed. I'm wondering if they may have flashed the ECU and replaced my Green Diesel tune because it seems a little down on power. There was no indication on the bill that they did anything other than replace the alternator and charged the battery. The next day, about 50 miles later the CEL comes on for the first time. There has been no change in the way the car starts and drives. I had to use the car and drove about 500 miles with the CEL on. Yesterday I checked the codes expecting an EGR related code. Instead I found 5 codes I've never seen before that seem unrelated.

P0504
P0513
P0560
P0688
P1252

I guess I have to take it back to the dealer but my confidence in their ability to fix it right is pretty low.
Has anyone had any experiences like this before?

I wonder if those codes simply relate to the loss of power as a couple of them (SKIM codes and boost pressure solenoid) it true would likely produce either a no start or radical loose of power respectively. Try clearing them and see if they stay gone.

As to ECU just ask them if they touched it.

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Sold to LOST member my 05 Ltd, GDE Stg II turbo + TCM tune, SunCoast TC w. Transgo kit, Steiger window regulators, Samcos, Fumoto valve, 2nd gen filter head with Lub. Spec. bleeder, Hayden clutch & 11 blade fan, inverted spare, P-1 battery, BF Goodrich Long Trail TAs, Etecno1 glow plugs, timing belt at 50K miles/8 yrs

Thanks for you help. As you suggested I cleared the codes and 4 of them went away and 1 new one showed up. So now I still have P1252 and P0299. In searching around it seems that P1252 could be caused by a solenoid and the P0299 may also be caused by this solenoid failing. I thinking that I might order this part since it's pretty cheap and see if that fixes it. If I take it to the dealer it will cost more just to scan the codes.

Can this solenoid just be unplugged until the new part arrives as someone suggested?