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If you have already converted those epubs in the past using calibre, there is no harm in doing another epub->epub conversion on them. If they are "original retail" versions then some people choose not to do that route and modify them using other means. If you are using default calibre settings then after a conversion calibre will have an original_epub (which is your file as it is now), and an epub version (the file after conversion), both attached to the same book record. So you can do the conversion and ee if you are happy with the result and if not just remove it. This is controllable via a calibre setting, if you have that turned off then the epub just replaces itself.
Modify ePub will automatically make whatever changes you tick in the options directly to the epub. And of the changes it is capable of making, certainly it can remove or insert the metadata jackets. Whether it can modify the cover depends on a number of factors - the "Update metadata (including cover)" option is the only one you can try at the moment. It does exactly the same to the epub as calibre would do when you choose Send to Device or Save to Disk, which is to update the internal metadata about the book, as well as attempt to replace the cover with the latest one you have in calibre. Note it can only do that cover modification if the cover is identifiable in te epub - which is a complex set of conditions but if the epub has been converted by calibre in the past then it won't be an issue.
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