When you delete a repository in Nexus Repo 2 it is moved to the global trash folder (sonatype-work/nexus/trash). This is done as a rename for efficiency. This leaves all files in the trash directory with their deployment time in the file's metadata. If you subsequently run an empty trash task configured to remove all items older than a certain number of days this will delete everything that was originally deployed before that number of days.
This is not the intent of the "purge items older than (days)" setting in the task. It should be based on the date the files were moved into the trash, not the date they were originally created.
Not that this only is a problem for the global trash directory, the per repository trash directory sets the deleted file timestamps to be the date+time of the deletion.