Please keep the list in the loop.
Did you read the manual as I suggested?
It says:
Bond atoms %d %d missing on proc %d at step %ld
One or both of 2 atoms needed to compute a particular bond are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the bond has blown apart and an atom is too
far away.
If you're saying the latter isn't the case, then it is the former.
Your cutoff (including neighbor skin) is too short for
a proc to find the other atom in the bond on another proc.
You can adjust this using the communicate ghost setting if
needed.
Steve