If you do this, make sure that you show (in the new stats) that the player is quarantined. If he simply disappears from the stats, affiliates will think you are shaving.
Most programs do this, though, and many can offer 35% or 40% flat without going under. That's why affiliates gravitate toward programs with no negative carryover, and that's why many affiliates threw a fit last year when a few programs tried to implement a retroactive quarantine system to keep more money for themselves.
What you are considering is a bit different, though, since you currently
do have negative carryover, but you should be aware that switching to "no negative carryover" with a quarantine system to limit the benefits of "no negative carryover" will make your program slightly less attractive than those that offer no negative carryover, no quarantine, and a high commission rate.