Why does Sublime-Text 3 overwrite settings?

Question

JSON

Desired settings:

{
  "font_size": 11,
  "theme": "Numix Dark.sublime-theme",
  "ignored_packages":
  [
    "Vintage"
  ]
}

But after changing the font size Ctrl + mouse wheel Sublime overwrites these i.e. erases other lines:

{
  "font_size": 12,
  "ignored_packages":
  [
    "Vintage"
  ]
}

Very inconvenient, you have to make settings in default .
Are there any solutions to this issue?

Answer 1

As far as I know, there is no way to solve this problem. If possible, please write in a comment! Thanks in advance!

Answer 2

And what is the point, supposedly the topic is dropped?
I don't have that problem. But he revealed something else:
The lines are returning to their places, as if he had cached the settings.