I think I ran into the same situation. I made an mxd with a related table. I made a AGOL MAP and the relates are there. But when I Hit SAVE AS and then make an application - basic viewer template - the relate isnt there.
I know people switch the terms AGOL MAP and APP when they talk, but can anyone verify they have an AGOL APP that has relates? I havent tried collector yet or WAB. And along those lines, if we use WAB directly from the AGOL screen on a smartphone, does the Relate work still?
Thanks,
Clint