My folder /etc/virtual/domain.com is empty. How can I rebuild it?

If, for whatever reason, you have your /etc/virtual/ folder for User , but still have other valid data in /etc/virtual that you don't want to lose, then you can re-set the default data with these commands:

cd /etc/virtual/domain.com

touch autoresponder.conf
touch filter
touch filter.conf
touch passwd
touch quota
touch vacation.conf
echo "user: user" > aliases
echo "*: :fail:" >> aliases
chown mail:mail *

mkdir -p majordomo
chmod 751 majordomo
chown majordomo:daemon majordomo

mkdir -p reply
chmod 700 reply
chown mail:mail reply

chown mail:mail .

Then you can start the process of re-adding all User accounts through DA, which are listed here

ls -la /home/user/imap/domain.com