Can you add a piece of pipe to the existing seep tube to get it back up where it needs to be.
YES. you can fill the seep tube with concrete, and put a siphon system in.
The picture you posted looked like you had a wide grade on the side. In an emergency you could get the dirt from that area and but it on top of the dam. The best thing would be have some dirt hauled in put in place and compacted.
Otto