theDucks gave you the short answer. I will give you a longer version
There is a whole subforum dedicated to plugins - take a look at the sticky posts within it for more info.
In the Modify ePub plugin as theDucks mentioned above if you want to replace a cover use the "Update metadata" option, and you will also see there is an option up the top right of the plugin screen of "Add/replace metadata jacket". Note that the adding/inserting metadata jacket functionality should "always" work with this plugin regardless of the ePub, it is the replacing of covers using "Update metadata" that will sometimes not be able to work for the reasons I mentioned above.
To answer your other "fears" I may have given you, doing an ePub->ePub (or any other) conversion is just a case of rolling the dice. Perhaps 9 out of 10 times it won't be give you the slightest issue (depending on your conversion settings and whether the book has been converted by calibre previously). And that 10th time it might not be an issue you personally care about. You can either accept that a small % of the time it may give you a less than ideal result and live with it (what most users do to be honest, be it due to ignorance or convenience). Or you can try to mitigate the risk by avoiding conversions unless you absolutely need to do them (preferred approach of others).
It all depends on the source of your books and how much you care about "preserving" them in the state they were originally edited (I am assuming retail ebooks here). Calibre has a habit of splitting pages where it shouldn't (I am not talking about the 260k limit, I mean between images that start chapters and the chapter text as an example). Depending on how the covers are defined you can end up with blank pages or pages with a questionmark due to a removed image. Margins are another thing that calibre loves to play with - which in many cases is a good thing but there are situations where you don't want them removed as the text is intentionally indented in the original.
These are not "life or death" things and some are recoverable with a bit of Sigil editing but for some people it is easier just to avoid it ever happening.