You can change the name of the proprietor in PEXA, by editing the information that comes through from the registry. For details on how to do this please refer to this article: https://community.pexa.com.au/t5/Help-Centre/Change-of-Name-Vendor-Help-Centre/ba-p/2891 You will note that there is an "Error in Register" justification reason, which would apply in your scenario.
However, as for the contract and the need to vary this and/or receive a Commissioner assessment, I am unable to advise. If a manual/Commissioner assessment is required, then yes, the dealing will become ineligible to settle on PEXA. You might be best placed reaching out to OSR/ROL direct to ask the query. I have attached here a link to OSR's listing of eligible dealings that might help for future reference: https://www.wa.gov.au/service/financial-management/taxation-and-duty/lodge-self-assess-and-pay-duty#econveyancing
Hope that helps
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