You can check what changes git sees by running git status in the ~/mailinabox folder. If you’re satisfied you’re not losing anything, run git reset --hard HEAD.
You should rerun the setup (curl -s https://mailinabox.email/setup.sh | sudo bash) after this, as it has not been executed yet.
The reason that the status check reports you’re up2date is because the version check works against the tag of the git repository. Apparently that has been updated to v75 even if not all your files are.