Customer sees 50 backup files on NetScaler GUI whereas same files are not visible on /var/ns_sys_backup directory. Whenever trying to delete the backup files from GUI it shows "ERROR: Backup file does not exist."

Manually updated the nsbackupmap.txt file to only include the files actually on the NetScaler and rebooted the NetScaler for the changes to take effect.

In this case the backups were being created and managed by using a script from SolarWinds. The script was incorrectly removing the files from SHELL, and needed to be updated to do so from NetScaler CLI, to prevent the issue from reoccurring.

Original SolarWinds backup script:

login
shell
cd /var/ns_sys_backup/
rm backup_full_10.0.0.100.tgz
exit
save c
create system backup backup_full_10.0.0.100 -level full
shell
scp /var/ns_sys_backup/backup_full_10.0.0.100.tgz user@10.0.0.101:backup_full_10.0.0.100.tgz

Corrected script to remove backup files from NetScaler CLI instead of SHELL so that the backup mapping list is correctly updated: 

login
rm system backup backup_full_10.0.0.100.tgz
save c
create system backup backup_full_10.0.0.100 -level full
shell
scp /var/ns_sys_backup/backup_full_10.0.0.100.tgz user@10.0.0.101:backup_full_10.0.0.100.tgz

Problem Cause

SolarWinds script used to create NetScaler Backups and remove older backups was not correctly removing the backup files, as it was doing so from the SHELL prompt. The NetScaler software is unaware of changes done in SHELL, therefore it will not update the backup mapping list (/var/ns_sys_backup/nsbackupmap.txt) to remove the deleted files.

Backup mapping list file was not being updated; therefore, it contained stale records for files that no longer existed on the NetScaler, hence they could not be "deleted" from GUI.