The export endpoint does not honor the field order as defined in the search query but you should be able to pass an array of fields as an argument - "f". This way you can dictate the fields and their order in the export results.
Assuming you are using Python SDK, the code may look something like this ...
result = service.get('search/jobs/export',
...
...
f=["field1","field2","field3",...],
...
...)
Hope this helps. If you are using another SDK and need help with that, feel free to email me - nluthra@splunk.com.
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