I suggest that you consider using the Fx2424. It supports 3 high speed counters. It has 23.5K words of programming space. Problem solved.
As to your question about buying two FMD88-10 PLCs and how this affects their programming memory, I am at a loss as to how to answer this question.
But consider this, I once owned 2 old VW automobiles but one of the engines was broken. I could swap the good engine between the cars and make either one run, but only one car at a time.
However, even if I fixed the broken engine, I never could figure out how to install both engines in one car to get 8-cylinder power.