My sibling ran into this issue once. I'm not sure if it's a setting or a default, but vscode would assume they were working in a blank repo until they made a commit.

Sounds like this person had the project (without source control) in another IDE, tried out VSCode, and it assumed that it was all 'changes'. I don't use VSCode, do I can't say for certain, but I know my sibling lost ~4 hours of project set up for the same reason (though they immediately realized it was their fault).