Endnotes are used in one document with footnotes (usually) for some good reason. One note type is used for different purpose than the other. (As jindroush said: "They're usually semantically different.") This is why information of note type should be preserved. (Despite they are in epub technically implemented in exactly same way...)
Preserved in some way. As reasonable solution seem to be different numbering and/or (better "and" then "or"
) separated blocks of texts for each note type. Footnotes in one list, endnotes in another.