I am not able to delete tracked time entries, even when the work items associated with those time entries have been deleted completely (they have also been removed from the trash bin). How can I remove those tracked times?
By default, only the user who has entered the time track can delete it. However, you can configure Timetracker settings to also allow roles other than the user who entered the time track to delete time. You can enable this ability in the "Configuration" tab -> "Settings" -> "Time Tracker System Settings":
These are the roles you can set in the "Role that can delete time" dropdown list: