While beryllium is toxic, I doubt a small nick in a tweeter poses a serious hazard. I wouldn't worry about that.
The problem of that flaw is it may degrade the ability of the diaphragm to move in a pistonic manner at high frequencies. You can measure the response to see if that is a problem, if you have a mic. Measure both speakers and see how their response differs for the exact same conditions.
Or, if you don't want to make that big of a deal out of it and do not have a mic, just play some sounds from each speaker individually. If that damaged tweeter does not sound like the intact tweeter, then have it replaced. If you can't tell the difference between either speaker no matter what you play, than it probably isn't worth worrying about.