Okay, that's very helpful.
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No. you will have to run ebook-convert in.mobi .mobi yourself.
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Let me make sure I understand the syntax here. What is the "in" in "in.mobi"? - is that the filename? So if I'm converting book.mobi, I just run 'ebook-convert book.mobi .mobi' - from within the Calibre library directory? And this has the effect of rebuilding the file with the metadata that I've already set in Calibre - replacing the old mobi file with the new? And Calibre will continue to see the new, converted mobi file in its library? Can you do the same thing using the GUI - a mobi to mobi conversion?
The fact that you can't tell whether the Send to Device operation will change the metadata on a particular mobi file is kind of a pain - no way to know if you need to do this mobi-to-mobi conversion before sending until you've tried sending and seen that the file on the device has the wrong metadata. But maybe there's no way around that. Or do most people just routinely do a mobi-to-mobi conversion on all their books?
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It's a valid criticism. I'm very guilty of not documenting anything I've worked on (the / path tag and field:false in the search are two major things that people don't know exist but keep asking for). The only part that gets documented even close to what it should is the command line interface.
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This is unfortunate, because it means that a lot of the features you work so hard on probably never get used, or only by a very few users; all that work deserves more. And it probably means the software has fewer users than it otherwise would, because it's not as accessible. I know I'm pretty techy, and comfortable with figuring out how software works, and yet I still get pretty frustrated with the lack of documentation and a central source of information about Calibre. I resisted using it for a while because I didn't understand a lot of the things people were talking about on the forum and couldn't find any explanations - even now that I use it, I still do a lot of things manually that Calibre could probably do for me, and Calibre's behavior sometimes baffles me (like with the mobi metadata).
It's a difficult problem, though, because only the developers know enough to be able to document all the features, and they're the ones who don't have time - or probably interest - in doing it.