Windows Defender + Quarantine + External Drive = Voodoo?

I had my 1TB external hard drive plugged into my computer last night, and Windows Defender popped up saying that it had detected "malware." Looking into this further, I discovered that it had "Quarantined" the offending item and recommended me to "Remove it immediately."

I knew that the file was actually harmless, but being the moron that I am, I accidently hit "Remove All" under the "Quarantined Items" category instead of "Allow All." However, I didn't think much of this at the time, because I knew that my external hard drive had already been unplugged beforehand, so I figured Windows Defender would be unable to delete the file as a result of this.

Unfortunately, it seems I was wrong, as I am now unable to find the file anywhere on my external hard drive. Clearly, what quarantine must have done is removed the offending file from it's original location (my external HD) and placed it somewhere on my Windows 8 hard drive away from the primary components of the OS.

However, this perplexes me greatly, because even if I had initially chosen to allow the file to remain, how could Windows Defender put the file back in its proper place if the external drive wasn't even plugged in anymore? Furthermore, how can I prevent Windows Defender from automatically quarantining anything it unjustly deems a threat? I know from personal experience that AVG does not behave like this on default...