I had very little luck with the various Apple approved methods of solving this issue. Nothing would appear on my Macbook’s iCloud Keychain even after very elaborate tricks to turn iCloud Keychain off and on.
What did work was that in frustration I airdropped a single web site password from my iPhone to my Macbook. Subsequently every password appeared in ...
I have just had a similar issue and since my file was a pdf downloaded from a webpage I thought that this could be the issue. Having deleted the kMDItemWhereFroms extended attribute the file synced in seconds:
xattr -d com.apple.metadata:kMDItemWhereFroms my_file_name.pdf