That just means that you need to be creative with shuttling data around. Web tracking identifiers can ride in on deep links for example, which are then persisted to user defaults. After these identifiers have accumulated from a few different sources you then have a reasonably high-confidence fingerprint of the user.

To help this along the app can do things like kick the user out to their main browser to do some routine thing, where cookies can be accessed. The user doesn’t need to deep link back to the app in that case, the app can pull down whatever tracking info was harvested during the page visit and persist it.