rewritten with choose file commands rather than path specifications. All I really meant for you to do was to edit in the the posix paths to the files you're working with, but this works just as well.
-- choose the file with the list of URLs to check
set fileOne to choose file with prompt "Choose URL list file"
-- choose the file with the HTML to search
set fileTwo to choose file with prompt "Choose file to be searched for URLs"
-- unused URLs will be saved in this file on the desktop
set outputFile to (POSIX path of (path to desktop from user domain)) & "missing urls.txt"
-- read the list file and the main file
set fileOneText to readfileOne
set fileTwoText to readfileTwo
-- open/create the output file for writing
set fp to open for accessoutputFile with write permission
repeat with thisurl in (paragraphs of fileOneText)
-- each paragraph in the list file is a single url, so check to see if it exists in the main file
if fileTwoText contains thisurl then
-- url exists, do what you like, if anything
else
-- url does not exist, write to output file on separate line
writethisurl & returntofp
end if
end repeat
close accessfp