A typical situation: An author registered on the RePEc Author Service has a working paper, listed on RePEc in his profile, that got published in a journal. Now that the publisher has provided the bibliographic information about this article to RePEc, the author can add it to his profile. What should he do about the working paper?
In an overwhelming majority of cases, the answer is: nothing! Indeed, most publishers accept that pre-prints, even post-prints, remain on authors´ home pages or institution repositories (what department working paper series are, for example). In case of doubt, see the SHERPA/RoMEO list. Thus, the author should not ask the paper to be removed from wherever it was put up.
Note: removing a paper from an author profile does not remove it from the database. It only makes the system learn that the author is not the author of this particular work. The consequences can be very annoying. For example, it becomes impossible for RePEc to recognize that these are two versions (pre-print and published) of the same work, as they appear to have different authors. Then, someone stumbling on the working paper will not find a link to the published version.
For authors caring about their ranking, there are even more adverse consequences from removing the working paper from the author profile. First, many working paper series have higher impact factors that journals. Second, the authors loose the download statistics of the working paper. Remember, working papers are much more downloaded than articles. And if the article is available only to subscribers, non-subscribers do not have the option of accessing the free working paper version.
And if it is really required that the working paper be removed, ask the RePEc series maintainer to only remove the link to the full text, not the whole record.