Bravo @Ben Spead! Glad to have connected at GS this year and look forward to many great conversations to come! 

Hi Kevin!

We've done this exact thing for our internal projects. At J2, we have a custom source control solution that works in both Studio and VS Code, and with both Subversion and Git (We use Gitlab). Our systems team was able to build a series of scripts to migrate our entire Subversion repository to Gitlab, while maintaining checkin history in the process.

Further investigation on this yields evidence that the VS Code plugin makes direct SQL injection calls when a project file is updated. This is different from how Studio does it. As a consequence, making changes to a project doesn't hit our source control hooks, which explains why we're running into this issue.