We have been facing this issue since a while on our servers. We are running the latest Xtrabackup rpms and use it to create a full backup on every Friday and then a differential backup on each day of the week. But since a while it is observed that as soon as the first differential backup is run over the full backup, the non-innodb tables (mysql,performance_schema etc) go missing from the full backup? The non-innodb tables are very well present in the full backup folder when full backup is taken and even until first differential is not run. After the first differential the enxt day, the tables go missing from full backup folder. Has anyone faced a similar issue in past? Would really appreciate some insight on this.