It is going to sound crazy, but I found this out.

Do you have a while loop inside the cy.readFile?

I had a while loop in my code which had nothing wrong with it...I made sure that it ran outside of the original script to check and even changes the logic so that it would only run one loop but...

When I had the while loop inside the cy.readFile it timedout

When I replaced the while loop with a for loop there was no problem.