I believe I have now found the issue.
The VSCode plugin is displaying Int64 values as double, when you make a change to a document with Int64 values and save those values are set to double.
It does appear to be a bug in the plugin, I have reproduced this problem on a few different databases/collections
To Reproduce
Save a document that contains an Int64 value.
Open the same document via the plugin.
Make a change to the document and save.
Any Int64 values are converted to double.