A. I think agents know what they’re getting into, so you don’t have to worry much.
Do your best with indents and you can even have a paragraph break (a blank line) to show changes in paragraphs if you’re really that worried. I don’t know about you, but my e-mail has the ability to itacilize words, so you may want to look over your submission and italicize anything that needs it – if the text got messed up in your cut & paste.
Much more worrisome than the formatting changes, at least in agents’ minds, is how writers use e-queries as an excuse to write really long queries. Just because it’s electronic doesn’t mean you get to skip the “one-page rule.” Keep it short and sweet, because a long query is a long query on paper or in e-mail.