fix(version): only update existing lockfile deps

[fahslaj]

Only update lockfile dependencies that already exist.

Description

Motivation and Context

This is a refinement of #3091.
Lerna workspaces that use bootstrap will not include their linked dependencies in package-lock.json, so the version operation should not add them in if it didn't already exist. This fix ensures that if the linked dependency already exists, it will be updated, but if it doesn't, then it will not be added.

How Has This Been Tested?

This has been tested manually as well as covered by appropriate unit tests.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Chore (change that has absolutely no effect on users)

Checklist:

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.