Have you and a colleague both simultaneously made changes to a document file? When you discover this, a decision must be made to keep one person's changes and discard, or manually paste in, the others'. Well, the same thing can happen between Bookdog and a web browser or other application.
Most web browsers, except Safari, ignore and overwrite any changes to your bookmarks file you make while using Bookdog. Obviously, this is also the case with online bookmarks storage services such as del.icio.us. Therefore, if, while using Bookdog, you use one of these browsers to visit a site, and then decide to make some changes (say, add a bookmark) using a browser or its bookmarks manager, you cannot "just do it". You must:
If you "just do" step 3, and then later want to save your work in Bookdog, Bookdog will tell you that you must choose between keeping the changes you made in the browser, or the changes you made in Bookdog, and lose the others' changes. You sometimes get this warning even if you do all three steps, since browsers are often making trivial changes to your bookmarks file as you browse, for example timestamping when you visit a site. In this case, if you know you have made more important changes in Bookdog, click Write.
By contrast, Safari and Bookdog behave cooperatively, watching the bookmarks file and re-reading any changes done by the other, so this problem does not occur. That is why, in Preferences > General > Browser to use when Visiting bookmarks, Bookdog recommends the Safari option for casual users.