Firstly, it's important to note that Calibre is not a DRM-removal tool. This is important, because in many countries it is of course illegal to write or distribute such tools, and Calibre doesn't break any laws. You may have added "plug-ins" to your Calibre installation that carry out that task, but they are not a part of Calibre!
If you want to re-add a book to your Calibre library, you can either delete the entire book and then re-add it, or you can just delete the format you want to replace, and then re-add that format. The latter is easier if you've spent time editing the metadata of the book, for example.
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