One item of background that I forgot to mention (since it's 
general, not specific to this area) is that they do have access to knowledge of our history and to our books and documents---it's not used all 
that much because it's fairly expensive, but most major church libraries (for example) would have copies of the "essential" books.
Astronomer wrote:
Though, it depends which kinds of denominations you have in your world.
Among the Chosen, probably most major denominations are represented. Among the natives, by this point "denomination" is an utterly foreign concept. (Not 
unknown, but thought of sort of the way Americans might think about British politics.)
Astronomer wrote:
Probably among a lot of those (Lutherans, Calvinists, Roman Catholic) it would be a lot of theological issues (the Trinity, Bible, Liturgy, Sacraments).
The Trinity is probably a non-issue, as it seems to have become in recent times here. The Bible---or, rather, the Apocrypha---probably would be simply because the disagreement persists in the Church here today. Liturgy is one of the topics I named originally, but is 
so broad a description ... Sacraments, however, I hadn't thought of.
Astronomer wrote:
If there were some of the later denominations which were even more radical than those, there might be a lot of more 'practical' issues (warfare, politics, etc).
Warfare ... since the Empire has at this point never 
started a war, and the Enemy is almost-but-not-quite analagous to Satan incarnate, so ... 

What do you mean by "politics"? (And what would "etc." expand to? 

)
Aratrea wrote:
What books of the Bible are included (aka, about the Apocrypha)
Like I said, that's not one I'd thought of, and it would indeed probably come up simply because the representatives from among the Chosen would have disagreement.
Aratrea wrote:
What the Lord's Supper is and at what age people should partake.
What baptism is and at what age people can be baptized.
And the sacraments, too, are a knot of issues that 
would come up, and that I hadn't thought of.
Aratrea wrote:
What happens at the end times (though I could see an argument for them deciding that wasn't as important so as to have an official position on it.)
This, of all the issues, is most amenable to "applied-metaphysical veridication," but in any case speculation about the end of one world wouldn't really be seen as an essential issue to debate in an ecumenical council in another.
Aratrea wrote:
If tradition should be held as near-equal to Scripture.
This 
would, most likely, come up---but the natives have their own set of "traditions of the Church" to complicate matters further 

Aratrea wrote:
If one is saved by faith alone or by faith and works.
Yes, that (and a whole host of other related issues) would come up. But I think that even phrasing the question like that would be somewhat foreign to the natives, which would help a resolution to be reached more quickly.
Aratrea wrote:
The Trinity.
Like I said above, while this was an issue in the early Church, it's a long-settled matter among us, and was probably similarly settled quite early in Imperial history, so I doubt it would come up (except that one of the first orders of business of the Council of Capitol might be to explicitly affirm the findings of the first several ecumenical councils (Nicea, Constantinople, Chalcedon, etc.)).
Aratrea wrote:
How the church should be governed (it could go a lot of ways here.)
Yes, that is in fact 
the issue that made the summoning of the Council of Capitol urgent: the Catholics and Anglicans/Episcopalians among the Chosen are now out of communication with Rome and Westminster, and all of the Chosen are accustomed to an utterly different form of Church organization (
denominations) than they find among the natives. But how the native church is organized, and what the Council would come up with, I don't know yet ...
Aratrea wrote:
And of course the classic freewill/predestination debate...
I don't think that'd be likely to come up, since it doesn't really have any practical implications on orthodoxy, orthopraxy, or ecclesiology.
Aratrea wrote:
Anyways, that's what I have from the top of my head.  Hope it helps!
Some good ideas I hadn't thought of.