Many times, my customers, have called me to remove "virus" protection software that itself, IS a virus or malware of some sort. I call it "extortion-ware". By the time you've clicked, "fix your computer now", you've done the damage..
But the question is , how do you know?
Most of the software that offers updates is in fact safe, but the key is, software that you've authorized, or is part of the OS, is safe to update. It is a safe bet that a Pop-Up that warns you about your files, being corrupted, and asks you to pay for or install the "full version" of a "cleaning" software, is probably malware. Do NOT click on that button!
Also, a common trick these hucksters use, is to offer a "yes" or "no" button, and pressing either one will do damage.
When you are not sure, do NOT click anything, but "x" out of the pop up, if you can.
As well, if you don't have critical data open, you could shut your computer down immediately. At the time of restart, run spyware, and virus scanning software, at this point hoping that it hasn't already infected your system.
Any time an "update" seems urgent, it probably will be dangerous to click to continue, Unless, you are fully aware of the software in question, hence your own virus software.