Yes, you can withdrawal without affecting your bonus.

I have been clearing the bonus playing 1/2 NL. I am clearing it about, and with multi-tabling get bonuses at about $11/hour. It can definitely be cleared, especially at the higher limits. Personally I feel like the massive size of the bonus more than makes up for the lack of clearance...I mean, $10,000 is a lot of money. And if your a decent player you'll make alot from playing as well. The games are certainly not as easy as Party, but I feel like they are still quite good. Overall, I recommend doing this if your able to set out a schedule and follow through, because clearing the whole thing is definitely worth it for that last $1,000.