If you go to WHM -> List Accounts and a lot of accounts are suddenly missing. This may be because cPanel has recently changed the minimum UID and GID that users are setup with. This setting used to be 500, and is now 1000.

Unfortunately if the script
/scripts/updateuserdomains --force --verbose
is run, it may only grab users with UIDs higher than 1000.

To fix this you need to modify the setting at /etc/login.defs

#
# Min/max values for automatic uid selection in useradd
#
UID_MIN 500
UID_MAX 60000

# System accounts
SYS_UID_MIN 201
SYS_UID_MAX 999

#
# Min/max values for automatic gid selection in groupadd
#
GID_MIN 500
GID_MAX 60000

After modifying that file, you can run the script again:
/scripts/updateuserdomains --force --verbose
This should update WHM with the correct information for all your accounts.