Revert "Cleanup flagging code for AggregateAtoms"

This reverts commit b9a873afa19814948e03bc2815e6d2f453bdd651.

Reason for revert: This is causing multiple test breakages which are showing up in presubmit

BugId: b/210308900

Change-Id: Ibe8c7ccd0a35a75e5ef606ede6959a854d7a4e1d
12 files changed