Now I’m really lost about what you’re doing.
the first thing is that if you export the code and put it into PHP you will completely loose the ability to update the field group through the ACF field group editor. This is going to create duplicate field group IDs and field keys and will likely cause strange things to happen.
I’ve tried recreating the field group you posted above and updating it, exporting it, returning to the field group, I’m not seeing any problems with it. I’ve even tried disabling the ACF javascrip to see if that could cause a problem.
The only thing that I can think of here is that some portion of your customization to the theme is causing the issue. You might want to comment it all out and test without it to see if you still have this problem. The only way that anyone is going to be able to help you is if you can figure out what’s causing this to happen and maybe looking at that code will help explain it.
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