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If you don't update underlying TDE file outside of Tableau (or sharing it across multiple workbooks) then you might want to try switching to TWBX files (packaged workbooks) which will create less contention around TDE files. Yes, we do lock it during certain operations.
Another thing to note - when you update an extract it's actually getting stored in a temp folder until workbook is saved - only at that point original extract file is getting replaced.
It is also possible that there's some lurking bug in this scenario so if you have more concrete steps I'd be happy to follow up more.