Hey guys, I'm having a disappearing messages issue too.
It usually happens when I'm sending a message to multiple people, or sometimes even when I'm just sending it to one person. After composing and sending the message and I go back to my inbox, all the messages are gone (I use GoSMS Pro); and when I go to the stock messages app, they're still missing.
That to me feels like it's an OS-related problem and there are multiple cases I've found online where it happens to other owners of newer Samsung Galaxy phones (S3 and Note2, not sure about S4 tho). I didn't have this problem when I first got my phone, it just started happening after one of the OTAs a month or two ago.
Restarting the phone fixes it, and that's what I used to do. I have found another way for me to get my text messages back: Call your own number (from the same phone with the missing messages). Obivously, you'll get a busy tone, but by calling my own number, my stock phone app will flicker for a bit, and it will crash ("the process com.android.phone has stopped"), restart, and then everything will be fine again.
Hopefully it works for you. This has led me to believe that the problem is under the hood and not caused by downloaded apps etc.
-- I reviewed some posts above and:
-I'm using Nova Launcher and I am getting this problem. I've never used Launcher8