It would be super handy if endnote would warn you if you already have an imported reference. I sometimes forget what I already have and go through carefully importing and polishing an import (correcting the envitable APA errors in the import etc) only to find I already have it.
If there is no mechanic to do this in endnote then I’ll just have to start checking my references every time I look for a new one, which is annoying 
If you are importing file(s) or folder(s) using Endnote’s “Import” feature [File > Import] there’s an option in the File Import dialog box to discard duplicates. If you are exporting records from an online database directly into an Endnote library there isn’t any automatic function at present to detect, warn, or prevent duplicate records. So you would subsequently have to run Endnote’s “Find Duplicates” function to locate and delete duplicate records.
You might consider posting a request in the Product Suggestions section of the forum.
If you are using the integrated library and online (the last icon) where every thing from every search is automatically imported into the library – you do have an option in preferences to not import those already in the library, but since I WOULD NEVER WANT TO import every reference from a search, it is pretty useless.
I obtain new records online into a temporary library, and then import that into my main library with the discard duplicates on.
I too wish (and I am sure it is there in suggestions somewhere already) that they would fix this issue.