Just because this issue has been going on forever, and seems bizarre that it still works like this.
https://community.shopify.com/post/2902183
Adding tags through admin pages (customer, order, etc) removes/overwrites any tags added by 3rd party (eg. by flow / apps / other users) whilst you have said admin page open. So instead of a simple tagsAdd mutation (which adds to, not removing, other tags), there’s no handling of additionally added tags, and it removes anything other than what a given user sees at the time they open the admin page and adds their own tag.
Why? Seriously, why? Who thought that was a good idea?