ADE reads PDF and epub files that are either DRM-free or are encrypted using Adobe's particular brand of DRM infection. Adobe Reader will read PDF only, and AFAIK only uninfected files. You should have been able to drag & drop the book into ADE, and then onto your device if it's authorized in ADE.
Where did you buy the file? If you got it from B&N (since you have a Nook), it wouldn't download into ADE, it would go into the B&N version. Were you able to open the file on your Nook? Usually you have to load books onto a reader through the software that it's encrypted for--ADE, B&N, etc. But I don't know how a Nook works for that.
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