Good question and thanks for reading about those upcoming changes (Collect will need to stop using /sdcard/odk for files)! Yes, this should all continue to work seamlessly. The only workflows that should be affected are the ones that involve direct access to ODK files such as pushing with adb or using other applications that integrate with Collect. Everything else should work the same.
We will be publishing a beta in the next few days with the storage change and would appreciate your help confirming that this is the case for functionality that you rely on. We're trying to test everything but Collect has a lot of different behavior that can sometimes combine in unexpected ways so getting some feedback from users is always much appreciated!