Subject says it all: Backup stops if a domain is deleted after backup starts, instead of continuing trying to backup other domains existing on the server:
This is what comes out in the email result of backup:
Virtual server DELETEDDOMAIN_HERE.com cannot be backed up as it has been deleted! <tt>setquota: user DELETEDDOMAIN_LINUX_USER_HERE does not exist. </tt> at ../web-lib-funcs.pl line 1427.