If Tortoise Git generates the appropriate shell change events for the files/folders then the icons should be updated. (Or at least re-requested; the result is again up to Tortoise Git, which may for example be caching the icon states. You can tell if that's the problem by using F5 to refresh the display. If the old overlays remain then there's a caching problem somewhere.)
In my experience, the icon update events are not always generated reliably by similar shell extensions, but when they are Opus should react to them and does here at least.
Make sure the whole Opus process is not UAC elevated as that would block the change notifications from reaching the process. (Similarly, make sure whatever is generating them is not elevated either, else non-elevated processes cannot have a two-way conversation with it.)