FLAG_ACTIVITY_CLEAR_TOPの API ドキュメントから
For example, consider a task consisting of the activities:
A, B, C, D. If D calls startActivity() with an Intent that
resolves to the component of activity B, then C and D
will be finished and B receive the given Intent,
resulting in the stack now being: A, B.
**The currently running instance of activity B in the above example
will either receive the new intent you are starting here in its
onNewIntent() method, or be itself finished and restarted with the new intent.**
ですから、あなたの活動自体は終了し、再開されたと思います。