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Calibre won't insert previous/next navigation - that would have to be built into the original source.
The only structure detection option that doesn't work on epub is the 'preprocess html to possibly improve structure detection'.
This is due to the way the conversion pipeline works and that Calibre treats OEB as a sort of 'reference' format. All filetypes are converted from their native format to OEB internally, and then re-converted from OEB to whatever the desired output format is. Preprocessing occurs BEFORE conversion to OEB.
Epub IS OEB, just in a zipped container. Therefore Calibre doesn't bother converting from epub to OEB, it just unzips it and goes from there. Because of this epub bypasses the preprocess stage of the conversion pipeline.
If you want the preprocess option to work on an epub just rename the epub to .zip instead of .epub and add a the zip back to the same book record as zipped html. HTML goes through the full conversion process, so it's eligible for preprocessing.
As far as preprocessing messing up your book formatting - I highly doubt it could have changed the order of the books contents - I don't see how this could even be possible. There's also no way it would insert next/previous.
That said, preprocess does look for potential chapter breaks in a fairly aggressive manner, and this can infrequently cause the book to be split in undesired places. It is also checking for line unwrap options and may change paragraphs, along with a variety of other things. While it's usually quite harmless and will generally improve a poorly formatted book, it can't be guaranteed to work for every single book. If you read the help/documentation it clearly states that preprocessing could make your book worse. This is the reason the default is disabled.
The other structure detection options that apply to epub and all other formats could also introduce new split points in the doc that aren't neccessarily desired. If it's doing something like that then you can tweak the 'insert page breaks before' option, or tweak the chapter detection xpath.
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