save proof independent settings, that are not used by the configuration

[PiIsRational]

Intended Change

Changes the saving behaviour of the proof independent settings, to keep settings that are not used by the loading KeY instance.

This also happens to fix a bug that was causing certain settings to not get saved properly when they were not opened
in KeY.

Type of pull request

• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• There are changes to the (Java) code

Ensuring quality

• I made sure that introduced/changed code is well documented (javadoc and inline comments).
• I have tested the feature as follows:
  created special settings and compared them to the same settings after saving them back from KeY

Additional information and contact(s)

@WolframPfeifer is involved in this pull request.

The contributions within this pull request are licensed under GPLv2 (only) for inclusion in KeY.

[codecov]

Codecov Report

❌ Patch coverage is 28.57143% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 47.98%. Comparing base (2aa39bb) to head (67ee871).
⚠️ Report is 12 commits behind head on main.

Files with missing lines	Patch %	Lines
...ka/ilkd/key/settings/ProofIndependentSettings.java	16.66%	6 Missing and 4 partials ⚠️

Additional details and impacted files

@@             Coverage Diff              @@
##               main    #3700      +/-   ##
============================================
- Coverage     47.99%   47.98%   -0.01%     
+ Complexity    16046    16044       -2     
============================================
  Files          1683     1683              
  Lines         96044    96048       +4     
  Branches      15387    15389       +2     
============================================
- Hits          46093    46092       -1     
- Misses        44681    44683       +2     
- Partials       5270     5273       +3     

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