How to backup email database of Apple Mail?
Why not let the export take three days or whatever is needed? That's the safe bet if you can't afford to lose mails. Also, the longer it takes to export, the more likely you have database issues or a volume of mail that demands a redundant backup in an industry standard format. 

Just like exercise, there may not be a quick and handy remedy to months of inaction. If you have years of mail, it might also be necessary to test restoring your normal backup before trusting the export. No one actually wants a backup, they ultimately hope to know they have a good restore chance.