In most browsers you will see a spinning wheel icon or some other indication that work is in progress and the server hasn’t yet returned a response.
Often, as when you load a typical web page, this completes in the space of a few seconds. A good litmus test then is to keep running the merge tool until you find it returns with that sort of snappiness – then run it one more time to be sure.
Of course, use your own judgement according to the speed of your browser, web connection and server – but if it is unable to find any duplicates then after hitting the merge button it ought to reload the page pretty sharpish.
Does that clarify things?