There appears to be very little online resources or help regarding this,I suggest please raise a ticket with tableau support if possible.
Thanks Bharat. I opened a ticket. I'll share the response when I get it.
I got the reply from Tableau tech support:
The hyper_db files is indeed safe to ignore or delete once the extract creation process is complete. The file is created by the API to compile and index the data before compressing it into the hyper format. As for why it isn't automatically deleted at that point, I could not find an answer. However, I can say that it will be overwritten by a new one the next time the API is run, or it will be created anew if it doesn't exist at that time.
One way to handle this, if the file needs to be removed, is to set an environment variable to control the location where the hyper_db file is created. Then a Windows task can be scheduled to clean out that directory periodically. The details for the environment variables that can be set are in this Online Help document:
Note: this document also explains that the file will be created in the current working directory if not variable is set.