I like to have a trash forum at my forums so here is how to do it:
1. Set up a Trash Forum, don't forget to untick "Allow new messages to be posted in this forum".
2. In library\XenForo\Model\Thread.php and In library\XenForo\Model\InlineMod\Thread.php change:
Now, every time you soft-delete a thread it will appear as a visible thread in the trash forum you created.
Permanently deleted threads are still permanently deleted