[aapt2] Fix finalized resources removal

The code used to expect all original staged resources to get
parsed before their finalized version. Looks like that's not the
actual case, and parsing code needs to expect those to come
later, and preserve the information that they aren't needed
anymore

Bug: 203779955
Test: manual, aapt2 dump resources <finalized framework SDK>
Change-Id: I6d9efe2eb7b406d05ca49a0a6ed745a1c509e2ef