Just to expand on this for those interested.
The Book Browser window is a view of the content of the book, not the directory structure of the EPUB. Presenting just a book view I assume made it easier to write in the beginning, and it is easier for users to work with.
Changing Sigil to allow access to a File Browser view of the EPUB is a major re-write of a lot of code, so its not something you will see anytime soon, or possibly not at all. It's being looked at, but only as a consideration.
Aside from that, there are certain rules in the EPUB specification about where files should and must go. META-INF is, according to the specification, only supposed to contain a limited number of specific files for the EPUB (container.xml, encryption.xml, etc.), and not just any random file (whether any reader is actually concerned if there are other files here is another matter). The important bit is that if you include your own files somewhere in the EPUB then they must be listed in the manifest section of the content.opf file (or whatever file the META-INF/container.xml file points to for the contents). And if they are html files they should also be listed in the spine section of the content.opf so they can be put in the right order.
If a file is not listed in the manifest, then it will not be seen or loaded by Sigil and will therefore be deleted from the EPUB when saving. (The exception being the apple .com file which is handled as a special case).
If a file is in the manifest but is non-standard (not html, not an image, etc.) then Sigil will display it in the Misc folder, but keep the file where it was when saving. If it's a standard file then it will be displayed in one of the normal Book Browser folders (Text, Styles, etc.).
So the answer to your question is that bookmark files aren't generally part of an EPUB and therefore aren't something that Sigil lets you edit. But if the bookmarks file is properly listed in the manifest, then you should see it in the Misc folder if its extension doesn't match one of the standard file types.
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