Q. Is it okay for “%” to be changed to “percent” in quoted text to match the rest of the document, similar to how you can change en dashes to em dashes in CMOS 12.7?
A. It’s better to leave the symbol as is. Readers who look for the original text of a quotation that includes “a 7 percent increase” may have trouble finding the relevant passage if it has “a 7% increase” instead—or, if not, they may wonder what other changes have been made without notice.
By comparison, dashes are dashes. A reader consulting the source of a quotation that included “a 7 percent increase—defying all expectations” is unlikely to be tripped up by finding “a 7 percent increase – defying all expectations.”
In other words, we consider the difference between dashes to be purely typographical, whereas the difference between “%” and “percent” is just beyond that threshold—more like a case of synonyms.