In STM 5.0, I see the same thing, where deleted resources still show up in the File Analysis Stats report. I think a good work around to filter out those that were deleted a long time ago is to create a my report based on the 'File Analysis Stats' report with a filter on 'Resource Name' not like the resource you deleted (I know this might be tedious and if you ever add that resource back, you will have to remember to remove the filter). Another is to filter on start time < sometime that seems appropriate (here, I wish we could put in systime because we could subtract some time value to get a time within the last week, month, etc but we cannot). I would not filter on no end time because you will filter out any File Analysis that has not completed.
I think this is a bug because I do not think I need to be concerned with a resource I am not monitoring anymore.
I hope this helps!
You can clear the fa stats report by running the following from a MySQL prompt: