Yeah, longer workouts can be a total slog and tough on the nether regions!
There is loads of useful info on some other posts about improving comfort, including things like saddle adjustment and even rocker plates. But in terms of your question I think you’re ok as long as you keep the breaks short and stick to the recovery valleys. Those long rides are, I believe, designed to improve muscular endurance so too long a break will impact that.
Have a read of the blog post below, it might be useful and includes info on pausing workouts
And here’s the forum chat on soreness ‘down below’