This is a bit late on the post for this problem, but I had this same thing happen a few times to me. I have the client on a VM that is there just to run import jobs. On 2 occasions the jobs disappeared and were not listed in the Import tab of the client. However they did exist in the hotfolder.xml file. Not sure what caused this as I am logged in as the same user (it is set to auto-login in fact) so that never changes. What worked for me was to set the Docuware Desktop Service to run as the domain account that was logged into the PC instead of Local System account. Once I then restarted the service and exited and restarted the client, the jobs all showed up.
Hope this helps someone.