MOBI to EPUBv2 or EPUBv3?

I have an older MOBI file that is converting to EPUB with content out of order.

The MOBI file is readable and flows correctly in the Calibre viewer. I've converted several other MOBI files that originate from the same time period to EPUB with no problem.

I figured out that converting using EPUB 3 worked. Is there a way to tell which format will work better beforehand, considering it's coming from a MOBI format?

Thanks!