Чтобы обойти ошибку нужно сделать на ноде:

sqlite3 /usr/local/mgr5/etc/ispmgrnode.db

sqlite> delete from isppackages where name="zip";
sqlite> delete from isppackages where name="unzip";
sqlite> delete from isppkginfo where name="zip";
sqlite> delete from isppkginfo where name="unzip";
sqlite>delete from ispfeatures where name="archivers";

затем killall core