There is no out of the box solution... Adobe's solutions really only include adding the App's ECID to outgoing URLs for your web to pick up the value and stitch users who move from your app to web as the same ECID... but there is currently no solution the other direction.
That said, if you can append the ECID to your deep links, your developers might be able to force the app ECID to match your web identity?
I think because Adobe came up with the Cross Device Stitching in CJA, they didn't continue trying to investigate better user stitching on AA... so I guess it's down to us to come up with our own creative solutions.