Fix scenario alternatives not removed correctly

[PiispaH]

When deletions were made in a scenario so that the rank order changed, all the scenario alternatives were not removed. This caused an error when the updated scen alt with the new rank number was attempted to be added back to the db.

Fixes spine-tools/Spine-Toolbox#2830

Checklist before merging

• [ ] Documentation (also in Toolbox repo) is up-to-date
• [ ] Release notes have been updated
• [x] Unit tests have been added/updated accordingly
• [x] Code has been formatted by black
• [x] Unit tests pass

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 78.28%. Comparing base (b0f789c) to head (af484db).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #418 +/- ## ======================================= Coverage 78.27% 78.28% ======================================= Files 72 72 Lines 9515 9517 +2 Branches 2033 2034 +1 ======================================= + Hits 7448 7450 +2 Misses 1731 1731 Partials 336 336 ```

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