Any good solution to your problem will keep the user informed of what is going on. A separate folder that contains archived bookmarks is a good start since it will keep the bookmark list tidy and free of broken links. It is possible, however, that a user might not understand why their link is gone from the list. Therefore I would suggest some sort of informational alert that tells them a bookmark has been moved. Something like this might be advisable:
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Here the user has been informed that a resource was deleted, which forced a bookmark to be archived. They can still see the bookmark in the archive folder, but cannot select it, reinforcing the idea that it no longer links to the content it is supposed to.
This kind of solution presumes that managers are not going through and deleting dozens of resources each day. Receiving that many notifications in the bookmarks view would quickly become annoying.