With missing coins I can definitely understand your frustration and worries. I haven't had the issue you have, although I did miss a lot of coins transferring from Cryptopia to my ETN wallet. Over a week I thought they had disappeared because my wallet update error. (Still doesn't want to update btw)

But making a small transaction TO cryptopia updated my wallet and showed those missing coins. So my guess is that your coins are somehow stuck in the blockchain but not lost.