When Plug in Git deploys it creates an entirely new theme and sets this as published. We do this so that the shop does not appear offline or broken during deployment.
If someone has unsaved changes in the Shopify theme editor, when the deployment completes and they try to save an error may be displayed in the Shopify theme editor preventing them from saving (since the theme ID they are editing no longer exists).
But note that it is not at all possible for saved changes made in the Shopify theme editor to be lost during deployment.
Therefore there's this window of only a couple of minutes during deploy when an error may be displayed in the Shopify theme editor for unsaved changes made after deployment starts.