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I am used to creating and editing .epub files, usually with Sigil. Sometimes, however, I need to retouch a file in .mobi format for my wife.
My usual approach is to convert it in .epub with Calibre, edit it, and then convert it back to .mobi, but I wonder if there is a quicker way which does not involve two conversions.
As far as I know .mobi files can't be edited directly, they have to be converted first to another editable format. So, no, you can't directly edit .mobi files in just one step. See this thread on MobileRead forums for further reference.
Anyway, I think that there is an easy a solution to your problem. Please note that in providing the following informations I have assumed that you are interested in using your eBook files with a Kindle device. If it is not the case, maybe not eveything will apply to tour particular situation.
Maybe you are already aware of this since you are a Calibre user, but it now has an integrated ebook editor that can work not only with .epub files but also with .azw3 ones (also known as KF8), which are used on Kindle devices. Here is a link to the Calibre manual page about this feature, where you can check if this is a tool that will do for you. It is rather similar to Sigil both in appearance and in functionalities, so you will have no problem to sort it out.
I know that strictly speaking an .azw3 is not a .mobi, but both these formats are mainly used on Kindle devices; moreover, as far as I know, for practical reasons (even if not for technical ones) the .azw3 format is considered to be a successor to .mobi; so, if you need to retouch your ebooks and have a rather recent Kindle device (or app), it should not make any great difference which one of these formats you will use on it.
Here are also some links to various resources that you may find useful:
What are you looking to edit? Content or basic metadata? If it is basic metadata, there is a program I have found and played with called MOBIeditor. It's written in .Net so you need Windows (the source code is available so you could grab that and compile it with Mono if you are running *nix/OSX).
It is very basic though, allowing you to edit only the following (I'll provide a screenshot to make it easier):
Since you're familiar with Sigil, you could install the KindleImport and KindleGen plugins.
If you've converted the .ePub files yourself to .mobi files, consider converting .ePub files in the future to .AZW3 files with Calibre. AZW3 files look better on Kindles and can be edited directly with Calibre. (Calibre packs an unpacks them on the fly in the background.)
