The recommendation in the release notes for robot 1.9.2 suggests to:
save your ontology with ROBOT 1.9.2 or Protégé 5.6.0 without introducing any changes to the logic or annotations, and commit the resulting ontology files
In my experience, that wasn't quite enough - complete canonicalization of my ontology didn't happen without round-tripping through OWL functional format - without doing that, some lines in the XML output were re-ordered when I round-tripped.
What worked for me (other variants might work too; haven't tested):
robot convert -i my-protege-5.5.0-ontology.owl -o my-ontology.ofn
robot convert -i my-ontology.ofn -o my-canonicalized-ontology.owl
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