Okay, here is my end goal.
To have awesome themes built using Builder (I don't like Editor, since it's changes are not portable). I can save then save different versions of these themes, upload them and customize across sites, saving lots of time and having the ability to make them look unique via Builder. Second, I want my sites connected in my wpmudev dashboard where I can make most to all plugin/theme updates with a click. That's a huge time saver and one of the things that most appeals to me.
Here are the issues I'm having that are interfering with that goal...
1. Updates do not get done. I just went through about 150 plugin/theme updates on my account sites and just 36 of them updated. I'm not sure why and would love your help figuring that out.
2. Updates are erasing my design. Look at arlingtonwainsurance.com and you'll see the contact icons I had added are now strange characters. I have seen other evidence that when I go to update a site that some of my changes in Builder are erased. I'm not entirely sure why. I upload the custom theme from my computer to then open in Builder. Is not the right way? After an update I can go into Editor and redo some of my customization, but Builder completely defaults to the original theme with no customization.
In short, I'm asking for help to see if I screwed something up with how I have added the sites in the dashboard. Most of them are on https (a recent change), perhaps that is goofing things up? Second, I'm asking to see where I am going wrong with Builder and themes and updates where I can edit the theme and not have the next update mess with those changes.
I'm sure these are errors I have made and look forward to your help in getting this to run well. Thanks!