I sent about 10.4 QCN to Poloniex yesterday as a test -- so verify I could transfer the coins properly, basically. Unfortunately, all has not gone well and while their support apparently looked into things and credited one of the deposits, the other six are still missing. Wait, seven deposits? Oh, yeah... I couldn't send one bigger transaction due to the old "too many inputs" problem. So I split it up into seven transactions (I just pressed the up arrow to repeat the last command, though I did generate a new payment ID after the first transfer). Here's the list of commands I used in the wallet:
I think it is risky to change the payment id while payments are still to be processed, are you sure Poloniex can handle that? They may only store one payment id per account/coin. Also, I wouldn't use an exchange transfer to cleanup dust, those transfers take longer and it just makes everything harder to track. Such a large transaction for such a small amount could sit around for a while before being included in a block, and may eventually be rejected and returned to your wallet.
I clean up small inputs by sending the coins back to the same wallet first, or a second wallet used for spending (the first used only for mining). Don't mine for pools where you are a tiny fraction of the pool hash (<1%), find a pool more suitable for your hash rate, until the pools have sorted out a solution for the dust problem.