I think I also just had the same problem. I was in the middle of working on my tableau workbook, and I had an exception error come up that it was unable to connect to my extract, which was on my c: drive. I checked the c: drive and the extract was no longer there. It somehow got deleted (not by me). I had to re-extract my data which was also from an SQL server table.
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First - my condolences as this is a difficult issue to deal with, especially if you have large data sources.
The cause appears to be around the metadata. If you don't have any folders or hierarchies built out, I don't believe it will happen. My feeling is it is around folders since the issue didn't occur prior to 8.1.
You create an extract with folders/metadata and then use this extract in a new workbook. Once you save with this new workbook it will delete the extract.
Either way, once it happens on your workbook, it will continue to delete the extract every time you save.
The solution to this is to open your new workbook, do a full refresh/extract and then from the file menu export packaged workbook. Do NOT save it (it will delete again of course). Close the workbook, open your newly minted exported workbook and you are good to go. From there you can save as tableau workbook again if you want and continue along your way and save as normal. The process of exporting it seems to bring over the folder/file/metadata structure.
I've reproduced this issue from scratch using the sales example data set. I am awesome - I can make extracts delete on the fly!