Files that have been deleted or upgraded to newer versions still show as existing when viewing a computer's inventory or running an inventory report.
When a file is upgraded or deleted, an NSE is sent up at the time Inventory detects the removal/upgrade that removes the row for that computer. If that removal does not occur for whatever reason (NSE is "lost", processing error, etc.) another NSE to remove it is never sent, resulting in the file still showing as present in Inventory.
The following process refreshes all file data on all systems. It is crucial to run a Full Inventory on all systems after the process to get all current file data back.