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In general, a MOBI>ePub conversion results in very few changes. The differences sometimes vary depending on the reader/app used to view the resulting ePub.
There is no way to predict what the differences may be since its a matter of exactly how the MOBI is constructed. In the end its just Trial and Terror. The most likely cause for a change is having a tag in the MOBI that is unstyled, thus relying on the reader's default behavior, and the resulting unstyled tag in the ePub displays differently due to the ePub reader's differing default behavior.
This type of change can show several ways. One involves paragraph indents and leading (vertical space between paragraphs). If you are using calibre for conversion and the first try is not what you like, a second conversion with different choices on the Look and Feel tab can usually resolve the issue.
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