No, Altera does not recommend that you have a mixed alloy reflow process. A mixed alloy reflow process is not easy to control. A reliable solder joint is one where the solder paste and the solder ball mix (at reflow temperatures) resulting in a consistant or homogeneous allow throughout the joint.
With a mixed allow reflow process, the mixing of the solder paste and solder ball is not consistent. The flux in a leaded solder paste will evaporate before it can remove all of the oxides in the lead-free solder ball. Leaded solder paste fluxes are formulated to clean the leaded solder balls at a lower temp (below 183C) where the lead-free solder balls need to be cleaned around (200C to 215C).