Fix resetting settings when saving

[Trial97]

fixes #1856
And most probably other issues where the setting was reset but persisted on save.

[TheKodeToad]

I haven't tested but this probably causes the state of columns being shown/hidden to be reset in some cases.

[Trial97]

I haven't tested but this probably causes the state of columns being shown/hidden to be reset in some cases.

It shouldn't. The clear happens on the written-in file settings, but their value should already be in memory as we want to write them, so unless we reset the setting that will not happen(also from my testing I could not reproduce it).
Please test it out but this should have no implication for the column state.
For column stuff look here: #1849

[TheKodeToad]

Oh, it should be fine. Unregistered settings will still be preserved, right?

[Trial97]

Unregistered settings will still be preserved, right?

So long they were saved before yes.
This PR only brings back the old functionality where on save the file was replaced instead of merged.

[github-actions]

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