Not sure exactly what you have going on there but here is a viable workaround..In Thunderbird,Account Settings / Server Settings,you can set up so what you delete goes to a folder of your choice versus the "Trash" folder. Have Thunderbird send your deleted emails to a folder other then Trash and the deleted emails will not be emptied from Trash cause they won't be in that folder.
By the way it may be a setting you have at your actual email service provider that is causing the emails to be deleted when you delete them in Thunderbird.