First had trouble respawning the dragon and changed the Y level one block higher in the level.dat and successfully respawned the dragon afterward. We have since killed the dragon twice more totalling 3 times and still only have the original end gateway.

I'm including a screenshot from the level.dat file. The ExitPortalLocation had Y: 65 when 1.10 launched and I changed it to Y: 66 which allowed respawning the ender dragon.

I noticed another ticket that sounds like a similar issue but I'm unsure if it's actually the same issue. MC-104736