There are 2 issues in case of primary server has 512 sector size, and secondary server has 4096 sector size

• You may see below message in the SQL server error log

There have been 170613760 misaligned log IOs which required falling back to synchronous IO.  The current IO is on file

• If you are using Log Shipping with standby mode on secondary server, standby mode may fail frequently.

Msg 9004, Level 16, State 6, Line 7
An error occurred while processing the log for database ‘MessageExchange_Sanpedro’. If possible, restore from backup. If a backup is not available, it might be necessary to rebuild the log.

Please check 4k and 512 basic concept in below url.

http://blogs.msdn.com/b/saponsqlserver/archive/2014/10/02/message-misaligned-log-ios-which-required-falling-back-to-synchronous-io-in-sql-server-error-log.aspx

http://blogs.msdn.com/b/psssql/archive/2011/01/13/sql-server-new-drives-use-4k-sector-size.aspx

http://blogs.msdn.com/b/psssql/archive/2013/05/15/sql-server-storage-spaces-vhdx-and-4k-sector-size.aspx

Solution

https://support.microsoft.com/en-us/kb/3009974 : I don’t know how it work internally. It might force the primary to 4K alignment. Please fully test it out and apply it.

Note After you apply this hotfix, you have to turn on the trace flag 1800 to make this hotfix work correctly.

https://support.microsoft.com/en-us/kb/2987585 : This one is great. Need to turn on trace flag 3057

Thanks Bob ward and Robert Dorr for investigation.