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It depends on the formats and the program used for conversion. Also, some formats have more features/options than others--if you convert epub to mobi, you'll lose whatever line spacing, fonts, and css features that were in the epub; converting back won't restore them because mobi doesn't have those options.
Converting through PDF is always a bad idea. PDF is a page-based format, and some PDF creation programs strip out formatting; their goal is to make a printable page, and the metadata that notes "paragraph" separate from "line placed this far down on the page" is missing. Converting from PDF can wind up with a return at the end of every line, depending on how the PDF was made.
If you have a file you want to be able to convert to multiple ebook formats, starting with a well-made HTML file is probably best. Converting around between ebook types, if there's anything more complex than bold, italics and chapter breaks, is likely to lose formatting info.
Some ebook formats don't even hold that much info; PalmDOC .pbd is basically plain text; if you convert to it, converting back out won't have the original formatting.
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