I had this same problem previously and asked a question in the forum:
Through the above, I was told that you cannot start editing in Builder and Switch to Upfront, or the system will get quite confused.
After all of that, I started an entirely NEW theme from scratch and began working on it solely in Builder. Then, once again changes I was making in Builder were not appearing on the live site (logged out). I realized that it was showing only what can be seen when I look at the site in Upfront. I imagine it's possible that when switching to the live site from admin, it went to Upfront instead since that can happen with some of the edit and customization links in WP if you don't go through Builder, however, I tried to be very cognizant of this possibility and *thought* I always tried to make sure I was in Builder.
Additionally, the top menu even shows one thing while in Upfront, and something else on the live site -- the menu is no longer nested with dropdowns, but all menu items are listed in one list.
Here's the thing: it shouldn't be this squirrely. The system should either work either way, in Upfront or Builder, or have safeguards against getting one getting screwed up with the other. It seems like a great system, and I've spent a good amount of time going through the manuals and the following the Upfront tutorial (https://premium.wpmudev.org/blog/upfront-1-0/), but I can't seem to get past go with this happening all the time.
Or, am I entirely missing something--am I not supposed to do certain things in Builder--does only the basic theme construction happen there, while the rest should be done in Upfront editor? If so, nowhere do I see this well explained. Honestly, I am not even sure what the difference between the two things IS other than Builder will allow you to export the theme easily. I HAVE noticed a few different things from one to the other, like Global Theme CSS selection does not appear in Builder, but without sitting and comparing everything directly, they seem virtually identical.
I really SO want to use this system and become proficient, but this is really getting frustrating.
I don't even know what support is supposed to do about it. It seems like I'm just stuck again and have to start over AGAIN, unless someone can tell me what it is I'm doing wrong, or fix what appears to me to be a problem with the system--as I said, it shouldn't be this easy for this to get all scrambled up. I can't be the only one having this problem.