A couple of HPL questions

[Your Computer]

1. Well, if they're within their own folders, then don't use those objects. If you've already used them and aren't certain which ones they are in your map, then you're bound to figure them out when other people are playing your story. As a last resort, you could back-up your stories and their content and then do a clean install of Amnesia.

2. Assuming you have everything organized within that one folder (unlike the custom stories you've mentioned in #1), then yes, you can just archive that one folder.