Low Memory -- if your BB is low on AppMemory, it may begin deleting things so as to preserve overall functionality.
Secondary Email Client -- if you have another email client (e.g., Outlook) that is removing emails from the server when it retrieves them, and if your email service is further capable of synchronizing Deleted Items with your BB, then it will dutifully remove them from your BB when they are removed from the server.
OK...I said a few...that's only two, but should give you plenty to look into in the meantime!
Occam's Razor nearly always applies when troubleshooting technology issues!
New to the Community? Click here and also here for helpful guidance. Also please click here for additional helpful information to guide you as you proceed. I always recommend that you treat your BlackBerry like any other computing device, including using a regular backup schedule...click here for an article with instructions. If anyone has been helpful to you, please show your appreciation by clicking the button. Need a reference to BB10 OS/SR versions? Click here. Need a specific BB10 AutoLoader? Send me a private message.