Would the compressed air put to much moisture In the system?

 

Yes, technically you can add moisture to the system by clearing the lines with compressed air, but consider that when you're replacing lines, they've already been swimming in air. Plus bleeding the brakes after you're done will replace the air with brake fluid. Unless you're pouring liquid water down the lines, I don't think you're at risk for any extreme water contamination.

And if there is a blockage in the line, make sure to disconnect the lines at your wheel cylinders, otherwise you could risk blowing that blockage into the wheel cylinder that you said you just replaced :P