Update iterators during aapt2 diff

A recent change broke aapt2 diff. We need to update the iterators when
an package, type, or entry is not missing from either APK.

Bug: 184066458
Test: `aapt2 diff` with framework before and after staging changes
Change-Id: I9138b9bd80aec24488feca6e06be1d7cf5775290