Could be so many things. On previous models you could let the battery drain and just replace it yourself with an aftermarket battery. My MK4 was like that, but a new battery only lasted about 1.5 years. Seems the MK7 does not like the electrical system touched. Did you let the ECM go to sleep before you unhooked the battery, then quickly replace the old battery with the new one? I don't think the ECM likes being without power. I venture to say the diagnostic and setup costs now will exceed what you would have paid a dealer to replace and setup a new OEM battery.
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