We need to change ontology so that mere synonyms are listed not as separated properties, but as (I would suggest) obo:hasExactSynonym annotations of canonical relations. The obo synonym annotation properties are also used by EDAM. We also need to attach the papers_with_code_id property of those relations to the canonical property instead.
SUGGESTION: Since this would be tedious to do fully manually, I suggest you simply mark all the 'synonym' metrics with refactor_comment 'synonym'. I can then write code so that the marked properties are automatically merged into their superproperties!