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Edit: On second hand; This is not the currect solution. However, filtering on expanded HasManyThrough is still not working.
HasManyThrough relations were not filterable. To recreate this issue you can use the following database from the Laravel documentation:
When recreated the above, the following query returns all projects instead of a any with a commit hash.
http://127.0.0.1:8000/odata/Projects?$expand=Deployments($filter=commit_hash eq 'XXX')&$filter=Deployments/any(s:s/commit_hash eq 'XXX')