I’ve got days on my calendar with two 90-minute zone 2 rides, for a total of 3 hours of base miles.
Am I losing the intended training effect if I split it up and do one in the morning and the other in the evening?
Should I just do them back-to-back as one workout?
Best if you can do them in one go. However, if you don’t have a three hour block of time to dedicate, you are ok with what you want to do.
From a running background with split efforts, short answer is you could lose a small % of benefit (and butt soreness), but miles in the legs will be equivalent and still beneficial. Beats putting it off or not doing it at all!
as @jmckenzieKOS and @CPT_A have said, better to do them your way than not at all.
As I understand it, the benefit of doing these rides back-to-back, is to do with your energy supply system. After a certain amount of time, you’re running on fat burn and by continuing the ride, you train your body to be more efficient at that - bit dependent on how much you take in during that ride. If you split it up, you start all over again and fat-burn kicks in later. I’m still reading up on this topic as it is also links to fasted rides (something I dread)
In the grand scheme of things, I don’t think it makes a lot of difference.
It is more beneficial to do them in one go as part of the benefit from endurance rides is the fat burning stimulus. When stopping at the cafe or breaking up the ride you ‘reset’ the fat burning a little and lose some of the overall benefit
+1
Thanks to all of you for the advice!
I’ll try to do it in one shot, but I’ve only ever had my butt on the trainer for two hours straight. Not sure how it will handle three continuous hours without a break.
Has anyone ever tried gluteal-administered novocaine?
not sure paralyzing your glutes would be my go-to plan. 
@Chaz Chamois cream is the way to go and also be sure to get out of the saddle when you can.