Albert declares attacks with a pair of D'Avenant Trappers. Nelson immediately pushes a Thallid Omnivore in front of one and a Saproling in front of the other, then says “Damage?” Albert says “Sure,” but Nelson immediately says “Before damage,” and tries to use the Omnivore's ability to eat the Saproling. Albert calls for a judge, as he believes they they have moved to the Combat Damage Step and it is too late for Nelson to save the Omnivore. How would you deal with this situation?

This is fine. Nelson is asking Albert if they have any effects before damage or if they are passing priority.

Exactly. I believe it is one of the more common ways how NAPs ask APs whether they have something to do or whether they are passing priority.

Anyway, I would separate the players and try to reconstruct what has actually happened. Also ask any possible spectators. The usual “has this happened before” questions etc. Maybe the NAP forgot about the ability and remembered only as they were about to bin the creatures. Maybe NAP was trying to fish for some action from AP. Who knows without investigating…

Since there is not a shortcut to jump from blockers to damage… and ask “Do something before damage?” involves the same “pass of priority” as ask “damage?” for AP… I'm OK for NAP to ask any of the forms.

AP want pass priority in both, and, in both, have a chance to do something if want to response the eat of the saprolin.

Without any investigation, if teoricaly all as post, I'm fine with NAP and how ask to pass priority.
Was very much more precise if NAP do:
NAP- damage?
AP - Yes
NAP - Them, as you pass priority, I do this. (eat the saprolin).
but, its ok

There's no problem here. NAP always gets priority last in a given step.

This came up at Canadian Nationals, and there was a reasonable amount of discussion about it. The consensus reached was that this was fine, though:

1) There is no established shortcut for “Damage?”
2) Nelson is supposed to have the last chance to respond before moving to damage, so he has not gained any advantage through this phrasing, even if it is ambiguous.
3) The speed of his actions indicates that he intended to sac the Saproling all along, so this is not a case where he made a mistake and now is trying to take it back.

Thanks for all the responses!