I changed the format from RIS to BibTeX & Removed the part that writes XML to the pdf because I have already done that using Jabref (which is much faster and more effective to write XML to the pdf files)

bookends-index_unlinked_group_dtpo.scpt

tell application "Bookends"
	tell front library window
		set theIDs to get id of publication items of group item "UnlinkedAttach"
		repeat with theID in theIDs
			try
				set myRefs to (publication items whose id is theID)
				set myItem to first item of myRefs
				set {theKey, thePath} to {citekey, path of attachment items} of myItem
				set theBIB to format myItem using "BibTex.fmt"
				
				set otid to AppleScript's text item delimiters
				set AppleScript's text item delimiters to linefeed
				set thePath to text items of thePath
				repeat with i in thePath
					set thisPath to i as string
					tell application "Finder" to set theName to name of (POSIX file thisPath as alias)
					set AppleScript's text item delimiters to otid
					
					tell application id "DNtp"
						set theDatabase to open database "Users/dwo000/Documents/Databases/DevonThink/Ling.dtBase2"
						set theLocation to create location "/Sources/@articles"
						set theRecord to indicate thisPath to theLocation
						set URL of theRecord to ("bookends://sonnysoftware.com/" & theID) as text
						set aliases of theRecord to theKey
						set comment of theRecord to theBIB
						set theLink to reference URL of theRecord
					end tell
					
				end repeat
				
				set user20 of myItem to theLink
				
			on error errorMessage
				
			end try
		end repeat
	end tell
end tell

I find no better script than this to link DEVONthink and Bookends.
Thank you Zach.