The by-the-books read is that you can re-roll all the dice that did not score hits on a single test. This means you no longer have 50% (or more) ones and no hits. Unless you re-roll a critical glitch.
OR, you can negate (entirely) the effects of a glitch or critical glitch. You keep whatever hits you have, and call it a day.
So in your example, when you spend a point of edge specifically to negate a critical glitch, you don't re-roll (you didn't chose that option), you simply don't have the effects of a critical glitch anymore.
By the book, I see no reason to ever simply negate the effects of a glitch / critical glitch vice re-rolling. The way I compensate for this is that you can spend edge to re-roll before I tell you what the effect of the glitch / critical glitch is, but if you (for whatever reason) wait until after I tell you the bad news, then you can only spend to negate.