That’s an interesting question. I suspect the workout benefit is geared more towards time in the saddle over actual power/distance. You’re training your body to handle to 3.5 hrs rather than trying to achieve a specific distance, etc. that in mind, I’d go for the full 3.5 indoors and adjust the resistance as required.
Hope one of the coaches jumps in on this one - I’d like to see an expert opinion!
Whenever I do a long outdoor session indoors I always ride the exact same amount of time. Despite discussions of trainer intensity equivalency, 3.5 hours of bike riding is still 3.5 hours of bike riding. There are physical and nutritional and planning benefits that you only get from actually riding that length of time. So even tho riding harder for 2.5 hours on a trainer may be considered by some to be the equivalent intensity of a 4 hour ride, it’s still not a 4 hour ride in length.
So my practice and suggestion is to still ride the full amount of time specified by the workout. At worst, you can either cut it short or dial down the intensity at the end, or ride it in level mode to allow yourself to manually adjust the intensity as you would when riding outside. That way you still get the benefits of riding long.
Because if your goal is to ride a Gran Fondo, you will want to practice riding for time, not just intensity, so you build up to get used to spending that much time in the saddle and all the benefits and planning strategies that come with it.