So is the symptom of the problem that the file no longer shows in the record, so apparently deleted, but your space is still used up when looking at the total attached files for the table or when using the QuickBase file manager tool?
If so, that sounds like a clear bug to me (but I would be interested to see the full response from support) as I'm not understanding what alternative Pipeline syntax they are suggesting.
A work around is to install the free native multi file upload Plug in from QuickBase's and have the user multi file upload files into a child table (as opposed to uploading into separate fields in the record). I don't know your actual use case, but the users may find that a better user experience to multi upload especially if it's pictures off a mobile device.
Then, when the files are no longer required, you can actually delete the records holding the file attachments, and that will surely delete the files.