I think you are just using Tableau Desktop to merge your files and generate it for exporting but.
I think its much better if you use Tableau Prep for your data processing and its the right tool
for the right job.
It is correct that if you have lot of joins, unions etc then extract may take lot of time to update. If possible you can do the data preparation at backend and load one file in Tableau which would be easier to handle. Also, check the below link if it helps: