I was having the same problem with non-deliverance to exchanges with couple of neoscrypt coins.
Just do a wallet repair > rebuild index. Wait few hours and your money will be in exchange.
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Can't be it. The transactions are visible in the blockchain. It's purely an issue with cryptopia not tracking them properly. It has nothing to do with your wallet.
Btw, my deposit from 3 days ago arrived today on cryptopia. Probably many other deposits also arrived hence the dump. They all put sell orders.
I would not hurry selling yet.