How do i reset the 2007 VW Eos roof?

If Your 2007 Volkswagen Eos has had its battery disconnected, it's possible that You'll need to do a window location relearn -- this is likely what You're looking for when You say a roof reset, since such a procedure doesn't exist. You can always fall back on manually opening and closing the roof if the following doesn't work for Your specific use case. You'll need to get in the EOS and turn the key to the ON position (without having the engine running). One at a time, put each of the windows to the fully up position, then tap up twice. Check the auto feature on that specific window. Then, move on to the next window until all are complete.