[CDF-24953] Fix node update (#1628)

# Description

See changelog below

## Changelog

- [x] Patch
- [ ] Minor
- [ ] Skip

## cdf

### Fixed

- When running `cdf deploy`, Toolkit no longer overwrites nodes that are
existing. Instead they are updated. This means if there is a property
that is not in the local configuration but is set in CDF, Toolkit will
not overwrite.

## templates

No changes.
