Why not just use a single teensy to do all the counting & comm ?
I will assume there is a valid reason for that. Questions to give more details about problem:
- Have you tried running the teensies at 3.5v - it may be a signal level issue.
- What is each teensy doing, who is keeping track of the pulse count - master Teensy 3.6 or Teensy 3.5 ?
- Is the output from the slave teensy 3.5 always good and the comm Teensy 3.6 messes up - where does the counts get corrupted ?
- How do the counts get corrupted, what issue are you seeing - what is expected result ?