"10xx" trains are, most of the time, used for either a "normal" train that has its schedule shifted so that two days' trains would show up somewhere during the same day or for trains that get "split" (e.g. the Eagle running over two separate sections of its route but with a bus bridge in the middle). For example, train 5 is due into Lincoln, NE just after midnight. When the train gets bumped two hours early, you'd end up with a train 5 due in at 0008 and one due in at 2208...and Arrow does not like that, so 1005 is used in lieu so as to make Arrow happy. You'll often see it on one day or the other surrounding a schedule shift (either temporary or permanent).
I think 1000-series trains also get used for Thanksgiving extras on the NEC, usually numbered for the extra sections they're running as part of.