Thanks for pointing this out, not sure how I missed it. Today, we successfully upgraded our management servers from R80.20 to R80.40 using Advanced Upgrade procedure (clean install from USB). Everything went well, I used the cp_log_export reconf command which worked...sort of. The updated log exporter was trying to access the certificates used for encryption in the old directory, and I then had to recopy the certificates to the new directory. I then ran the command to update the config for the exporter and everything was good.
Dave