VSCode/Git over 5k new changes in BranchA: commit, then switch to BranchB and untracked changes show up

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I am in the process of moving over a massive project from and old Source Control(TFS).The scenario is that I have made changes and additions to over 5,000 files in BranchA. I finished my changes and committed and synced the changes. I then change to BranchB in VSCode and I get the over 5k warning. Those changes should not have carried to BranchB as they are solely intended for BranchA at the moment and will later be merged into BranchB when the time comes. Why would the files have not been tracked only to BranchA and is there any settings to resolve this.

While in BranchB git reset --hard does not appear to work with the amount of changes that it is detecting. The undo changes button in VSCode does nothing either.

Thanks!

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