Fix edge cases in json version file updates

[adamzip]

Currently, the Json Merger logic of the dependency update part of codeflows does not differentiate between a deleted json file, or an existing json file with no content. This can lead to a few edge cases.

Eg:

1. The entire content of dotnet-tools.json is deleted on the VMR side. When it flows to the repo, the Json Merger will consider it as a deleted file, and will delete dotnet-tools.json on the repo side, leading to a small permanent divergence between the VMR and the repo

Note: this might be a rare edge case that has little impact even if it does happen