Fix undoing node removal

[farmaazon]

Pull Request Description

Fixes #9314

The node deletion does not remove AST node from the module, only unpin it from its parent; so undoing does not add this node, just modify it, and thus we weren't informed about metadata change.

Important Notes

Checklist

Please ensure that the following checklist has been satisfied before submitting the PR:

• The documentation has been updated, if necessary.
• [ ] Screenshots/screencasts have been attached, if there are any visual changes. For interactive or animated visual changes, a screencast is preferred.
• All code follows the
  Scala,
  Java,
  and
  Rust
  style guides. In case you are using a language not listed above, follow the Rust style guide.
• All code has been tested:
  • Unit tests have been written where possible.
  • If GUI codebase was changed, the GUI was tested when built using ./run ide build.