config saving: pop element from list error

(reported by @berruyer )

Removing an element from a list, and saving config, produces a list with duplicated element:

name: rw_test
test: this is just a test.
# comment1
one:
- pink: martini # comment2
  red: apples  # comment3
  blue: berry # comment4
two:
- a: true
  # comment5
  b: false
  c: null
three:
  - a
  - b   <<<< REMOVING b makes the three == ['a','c','c']
  - c