Option to delete existing prefix folder

[mfathollahzadeh]

Fixes # .

Pull Request Description

This fix should skip the optional deletion of prefix folder if the --missingonly flag is active.

Checklist

Not all may apply

• [ ] Code changes (must work)
• [ ] Tests exercising your feature/bug fix (check coverage report on Checks -> BuildStockBatch Tests -> Artifacts)
• [ ] Coverage has increased or at least not decreased. Update minimum_coverage in .github/workflows/coverage.yml as necessary.
• [ ] All other unit and integration tests passing
• [ ] Update validation for project config yaml file changes
• [ ] Update existing documentation
• [ ] Run a small batch run on Kestrel/Eagle to make sure it all works if you made changes that will affect Kestrel/Eagle
• [ ] Add to the changelog_dev.rst file and propose migration text in the pull request