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As a general rule to be safe you should only convert when you "have" to, such as shifting format. A lot of the time, the changes calibre makes during a conversion are not going to be visually noticeable when you read the book, which is all the majority of people care about.
There are a small number of purists like JSWolf who will post ultimatums of thou shalt not convert with calibre. Bear in mind that many of the reasons given for this are things that no reader of a book cares about in the slightest. People do not care what a cover image gets renamed to, what a style is called, or the file structure inside the ePub. These things have zero impact on readability. The only people who might care are people authoring an ebook, but they would have no need to do a calibre conversion.
However like any software calibre does have bugs, gaps in handling certain edge cases and on rare occasions conversion regressions in a new release. Kovid kindly stomps on bugs when reported of course, I've recently fed him a whole bunch of examples of issues i found with cover identification leading to broken images and broken TOC links which have been fixed in 0.8.55. However there are still other issues that can come up that do visibly affect the book, some of which are dependant on what your default calibre settings are (like losing margin based sub paragraph indentation) and others you cannot (splitting pages between images and heading styles, creating extra page turns in your book where there shouldn't be any). Doubled up cover images, multiple TOC pages, i am sure there are other examples I have forgotten, and that is all assuming you haven't done something really dangerous like enabling heuristics or changing various other default settings.
There will always be edge cases where *visually* bad things might happen. Risking a conversion just to put metadata inside the book is really not a sensible thing to do - most of the time you will ge fine, but why take the risk? Calibre already has a different mechanism to update the metadata when you save to disk or send to device exporting from calibre. The Modify ePub plugin came about as a way to apply such a change to books in your library in place, just so people could use the calibre viewer to read them.
No such in place option currently exists for mobi though to be honest I think there is less of a use case for it. Someone who only keeps mobi formats is presumably only doing this because they own a Kindle, in which case they will be reading their books on that device. However the Kindle ignores all metadata except cover, title, author and published date anyways, and calibre will update those when you send to device. Due to its limitations, no one should be keeping mobi format instead of ePub if they dont have to for device purposes, ePub is a far superior format.
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