In Illa Ecclesia
In illa ecclesia is a prepositional phrase. The flag is, of course, in.
Because of that preposition, illa ecclesia is in the ablative case.
This puts ecclesia as the main noun, and it is a type one, feminine singular noun.
Illa is a demonstrative pronoun, agreeing with and modifying ecclesia, so it is ablative singular too.
Put it all together and you get in that (particular) church.
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