Message+ syncing is hit and miss. For example, I use Message+ on my Android phone (Moto Pure X, before that Galaxy S5), my Android tablet (Samsung Tab4) and my Asus laptop running Windows 10. When I delete messages from my laptop, those messages are usually not deleted from my Android devices. Right now, as a test, I have 12 messages on my phone but only 2 on my laptop. There are so few settings on the PC version of Message+ that I find it hard to believe that I've missed something, but I'm willing to give your suggestions a try.