I know there are custom worlds that come with single file of necessary CC collection. What if I already have another single file of CC collection for another world that share some of the items. Is it ok to have those duplication? or is there a way to separate items in those single cc collections and should I delete those duplicated items before I put in my mods folder?

CC that shares the same resources will just override each other so it should be fine. However it will still read the resources which adds to your load times so it's best to try not to have dupes. There's no way to unmerge merged packages though unless you have all the single flies that were merged so you're stuck with the dupes if not. If you do delphy's dashboard can find duplicates and make weeding them out easier.

Thanks, chain! I guess it’s better to download single files and merge them myself to avoid those dupes.