Sql-server – sp_AllNightLog – running on an existing SQL server

It just seems so fragile.

Logshipping is tested and proved since sql server 2000 (and even older) days. Its not fragile.

Look at the errors ...

Last Restored File: \server\folder\db_20160105060002.trn,

Logshipping is trying to restore

Destination: '\server\folder\db_20160105080001.trn'

This means you have a gap in the log sequence. There might be adhoc log backups happening which is breaking the log chain.

Refer to my answer - How does Log shipping knows to keep track.

You can even Restrict users to COPY ONLY log backups, so that adhoc log backups wont break the log chain. Also,

@Spörri made a valid point to disable SQL VSS writer service, so that 3rd party backup tool cannot interact with SQL. Its a pain to find that out, since 3rd party softwares are crazy sometimes !

To find out gaps in your log backups, you can use below query

SELECT 
    s.database_name,s.backup_finish_date,y.physical_device_name
FROM 
    msdb..backupset AS s INNER JOIN
    msdb..backupfile AS f ON f.backup_set_id = s.backup_set_id INNER JOIN
    msdb..backupmediaset AS m ON s.media_set_id = m.media_set_id INNER JOIN
    msdb..backupmediafamily AS y ON m.media_set_id = y.media_set_id
WHERE 
    (s.database_name = 'databaseNamePrimaryServer')
ORDER BY 
    s.backup_finish_date DESC;

Another useful query:

-- http://sqlblog.com/blogs/tibor_karaszi/archive/2014/11/03/can-you-restore-from-your-backups-are-you-sure.aspx
-- modified by Kin to include backup start and finish dates
SELECT TOP(100)
database_name
,CASE bs.TYPE
   WHEN 'D' THEN 'Full'
   WHEN 'I' THEN 'Differential'
   WHEN 'L' THEN 'Log'
   WHEN 'F' THEN 'File or filegroup'
   WHEN 'G' THEN 'Differential file '
   WHEN 'P' THEN 'Partial'
   WHEN 'Q' THEN 'Differential partial'
END AS backup_type
,bs.is_copy_only
,bs.is_snapshot
,bs.backup_start_date
,bs.backup_finish_date
,DATEDIFF(SECOND, bs.backup_start_date, bs.backup_finish_date) AS backup_time_sec
,mf.physical_device_name
,bs.database_name
FROM msdb.dbo.backupset AS bs
  INNER JOIN msdb.dbo.backupmediafamily AS mf ON bs.media_set_id = mf.media_set_id  
  where database_name = 'master' -- change here for your database 
ORDER BY backup_finish_date DESC;

Besides being unaware that your backup is being performed as a COPY_ONLY backup instead of not being backed up at all, are there any caveats that anyone can think of if this switch is set to default Y or even if it's used at all?

A COPY_ONLY full backup is still a full backup. The only difference between the two is the COPY_ONLY will not reset certain tracking bitmaps. This means your differential backups will eventually be the size of your database.

https://docs.microsoft.com/en-us/sql/relational-databases/backup-restore/copy-only-backups-sql-server