The only way i can understand the warning, is if someone creates a qt-wallet, imports 5 BTC to it from a paper pk, spends 1 BTC from the qt-wallet, and then expects to be able to import the "remaining" 4 BTC to another clean wallet from the same paper pk. (assuming that the money co-exists in both the qt and paper wallet)
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This is exactly what the warning is attempting to state. There are many who try to use a "paper wallet" without understanding how bitcoin works and how transactions are structured. People have lost bitcoins because they assued that they could send 10 BTC to the paper wallet, then import that private key just long enough to create a transaction to spend a portion of it, then immediately delete the Bitcoin-Qt wallet.dat file. They didn't realize that the transaction would send the "change" to a new address and that the entire balance of the previously received transaction would be spent.
Yes.