Hi jamjen,
What is the "Action" which was taken on the file? If it was "Cleaned by deletion" or "Quarantined", then you should not see the file in the temp folder. You should consult the risk logs in order to find out the action which SEP took on the file.
EDIT:
As far as I know, the files, should they still exist, should not be hidden.
Also, try following the steps in the following document. It will most likely clear up the issue you are seeing with the .tmp file detections.
Title: 'Large amounts of temp files are being created in the xfer_tmp or 7.5/xfer folder and are being detected as threats.'
Document ID: 2009042217073548
> Web URL:
http://service1.symantec.com/SUPPORT/ent-security.nsf/docid/2009042217073548?Open&seg=ent
Please let me know whether following the steps in the document above resolves the issue for you.
Regards,
James