For anyone interested, each private key is filled with .00001 transactions. You can only transfer about 675 inputs out at at time, which is about $1 in BTC after fees. You spend your time selecting inputs and waiting for the wallet to manage the enormous amount of inputs. By sending BTC you are feeding the test and delaying transactions.
I need to transfer some BTC of Poloniex to a cold wallet. Is there any problem doing that while all this is going on ? (If it's a regular transaction - not one with hundreds of inputs and outputs).