Simulating file drop for windows desktop application

If this feature was mine to test, I would leave it for the manual testing.  This feature isn't likely to change very often, so frequent regression testing isn't necessary.  All the outside influences you mentioned do make it difficult to automate, so spending the time on automation vs. an occasional manual test isn't a good investment.  Create some test download files to cover the cases, save those in a safe place, and use those each time for a quick manual test.