As per the documentation, the coordinates of an atom written to a file by the dump command may not be in the simulation box, depending on when the last neighbor-list calculation was performed.
What image flags do such atoms get? Do they receive a new revised flag since they crossed the boundary? Or do theirs remain unchanged because they were not shifted back via periodic boundary conditions?
Did I miss this information in the documentation? If not, could it be clarified there?
A quick examination of one of my dump files tells me that the image flags do not change for such excursions. But is that the standard, coded behaviour?
The image flags remain unchanged. That is the whole point. Atoms are only wrapped back into the simulation box on neighbor list Updates and then also the image flags get updated, if needed.
Beyond that you can enforce strict PBC compliance with the dump_modify command which creates a temporary copy of the coordinates and applies PBC enforcement and image flag updates but incurs a performance penalty.
Normally, there should be no problem from atoms being outside the box.