An alternative is to use UI scripting to actually do a paste. Something like 
this:

set the clipboard to theFile
tell application "BibDesk" 
        activate
         set docName to name of front document
        set index of window docName to 1
end tell
tell application "System Events"
        tell process "BibDesk"
                set focused of table 1 of scroll area 1 of splitter group 1 of 
splitter group 1 of window docName to true
                keystroke "v" using command down
        end tell
end tell


Christiaan


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