I had the same issues. I eventually did upgrade and all seems okay, but every update gives the same type of errors (oc_ is my tableprefix):
(the latest update - 9.0.52.0 --> 9.0.53.)
dav: An exception occurred while executing ‘CREATE TABLE oc_addressbooks (id BIGINT UNSIGNED AUTO_INCREMENT NOT NULL, principaluri VARCHAR(255) DEFAULT NULL, displayname VARCHAR(255) DEFAULT NULL, uri VARCHAR(255) DEFAULT NULL, description VARCHAR(255) DEFAULT NULL, synctoken INT UNSIGNED DEFAULT 1 NOT NULL, UNIQUE INDEX addressbook_index (principaluri, uri), PRIMARY KEY(id)) DEFAULT CHARACTER SET utf8 COLLATE utf8_bin ENGINE = InnoDB’:
SQLSTATE[42S01]: Base table or view already exists: 1050 Table ‘oc_addressbooks’ already exists
notifications: An exception occurred while executing ‘CREATE TABLE oc_notifications (notification_id INT AUTO_INCREMENT NOT NULL, app VARCHAR(32) NOT NULL, user VARCHAR(64) NOT NULL, timestamp INT DEFAULT 0 NOT NULL, object_type VARCHAR(64) NOT NULL, object_id VARCHAR(64) NOT NULL, subject VARCHAR(64) NOT NULL, subject_parameters LONGTEXT DEFAULT NULL, message VARCHAR(64) DEFAULT NULL, message_parameters LONGTEXT DEFAULT NULL, link VARCHAR(4000) DEFAULT NULL, actions LONGTEXT DEFAULT NULL, INDEX oc_notifications_app (app), INDEX oc_notifications_user (user), INDEX oc_notifications_timestamp (timestamp), INDEX oc_notifications_object (object_type, object_id), PRIMARY KEY(notification_id)) DEFAULT CHARACTER SET utf8 COLLATE utf8_bin ENGINE = InnoDB’:
SQLSTATE[42S01]: Base table or view already exists: 1050 Table ‘oc_notifications’ already exists
federation: An exception occurred while executing ‘CREATE TABLE oc_trusted_servers (id INT AUTO_INCREMENT NOT NULL, url VARCHAR(512) NOT NULL COMMENT ‘Url of trusted server’, url_hash VARCHAR(255) DEFAULT ‘’ NOT NULL COMMENT ‘sha1 hash of the url without the protocol’, token VARCHAR(128) DEFAULT NULL COMMENT ‘token used to exchange the shared secret’, shared_secret VARCHAR(256) DEFAULT NULL COMMENT ‘shared secret used to authenticate’, status INT DEFAULT 2 NOT NULL COMMENT ‘current status of the connection’, sync_token VARCHAR(512) DEFAULT NULL COMMENT ‘cardDav sync token’, UNIQUE INDEX url_hash (url_hash), PRIMARY KEY(id)) DEFAULT CHARACTER SET utf8 COLLATE utf8_bin ENGINE = InnoDB’:
SQLSTATE[42S01]: Base table or view already exists: 1050 Table ‘oc_trusted_servers’ already exists