Master pages are a little strange that way. Basically, if you alter any master page item in your document, it becomes sort of detached from the master page.
For example, create a blank text box on your master page, then, in your document, add a few pages based on that page. If, in one of your document pages, you add some text, then delete the text box from the master page, only the text boxes without text will be deleted.
However, some operations will still work on altered items. If, instead of deleting the text box, you simply move or resize it, then it will affect all the text boxes in your document.
So basically, any operation on a master page that will potentially destroy work you've manually done to document pages will be ignored. Anything else will probably be ok. I'm sure there's an exception to this, but I can't think of one right now!