storyline 360 users are opening an old pdf version but we can't find it in storyline to delete it

A PDF can be added as either...

A resource (check your resource panel in the player settings)

A link (check each slides trigger panel for an open link trigger)

A webfile (check each slide for a web object)

You can also examine the Zip file and see if there are any old files in the 'story_content' folder.