Hi Paul,
Thank you for posting in Symantec community.
I would be glad to answer your query.
You are just one release behind than the latest one. Though it's recommend to use the latst version I would love to stay on the existing version unless I have not been affected by any particular issue which has a fix in the upgrade or want to use particular feature which is not available in the existing version.
Next release, SEP 12.1 RU6 is in beta testing & might release in next 1-2 month.
However,
1. Should I run the upgrade to 12.1.5 on both servers at the same time, or do the master first, then the other SEPM?
--> Stop the Services on both the SEPM, upgrade master first then secondary.
In case replication is configured, Symantec Endpoint Protection 12.1 and later does not require that you turn off replication before you upgrade. Symantec Endpoint Protection 12.1 and later does not allow replication if the database schema versions do not match.
2. I have approx 12,600 clients can anyone give an idea on upgrade completion time scale. I have read that it can take up to 4 hours?
--> SEPM upgrade should not take more than 30 minutes, client upgrade process may take longer depending upon methond you choose to upgrade all clients.
You must test the client upgrade process before you attempt to upgrade a large number of clients in your production network. If you do not have a test network, you can create a test group. You can add a few non-critical clients to the test group and upgrade them by using AutoUpgrade. You can confirm the upgrade completed successfully by verifying the version number of the client software that appears in the About dialog box.
It's always recommended to have Symantec Endpoint Protection Manager and SEP clients on the same version.
3. Should I be aware of anything else that may not have been mentioned in the pre upgrade doc from Symantec, or do you have any other tips to help me?
--> Few issues have been reported after an upgrade to 12.1 RU5 but not necessary those will occur in your environment also. To find more details check the following articles.
Known issues with SEP 12.1 RU5:
When Symantec Endpoint Protection 12.1 RU5 is installed on an operating system running within a VMware Virtual environment, several problems are encountered
http://www.symantec.com/docs/TECH214756">http://www.symantec.com/docs/TECH214756">http://www.symantec.com/docs/TECH214756
Editing the Scan Type of an existing Folder exclusion in SEP 12.1 RU5 does not save properly
http://www.symantec.com/docs/TECH224732">http://www.symantec.com/docs/TECH224732">http://www.symantec.com/docs/TECH224732
Installation of Symantec Endpoint Protection 12.1 RU5 fails with error "3- PAR signature failure, not running 3-PAR"
http://www.symantec.com/docs/TECH210498">http://www.symantec.com/docs/TECH210498">http://www.symantec.com/docs/TECH210498
Replication fails after upgrade to SEPM 12.1 RU5
http://www.symantec.com/docs/TECH225412">http://www.symantec.com/docs/TECH225412">http://www.symantec.com/docs/TECH225412
Follow best practices for upgrading or migrating to Symantec Endpoint Protection 12.1.5 (RU5) & Here is the latest best practice article for SEP 12.1 RU5 (12.1.5337.5000)
http://www.symantec.com/docs/TECH224034">http://www.symantec.com/docs/TECH224034">http://www.symantec.com/docs/TECH224034
Prior to start upgrade you must take necessary backups as a plan B to perform disaster recovery if upgrade failed.
To take recommended backups follow this article: http://www.symantec.com/docs/TECH160736">http://www.symantec.com/docs/TECH160736">http://www.symantec.com/docs/TECH160736
Prior to start an upgrade go through the System requirements: http://www.symantec.com/business/support/index?page=content&id=TECH224712">http://www.symantec.com/business/support/index?page=content&id=TECH224712">http://www.symantec.com/business/support/index?page=content&id=TECH224712
Here you can see upgrade overview guide: https://www-secure.symantec.com/connect/articles/upgrade-overview-sep-121-release-update-5-121533750...">https://www-secure.symantec.com/connect/articles/upgrade-overview-sep-121-release-update-5-12153375000">https://www-secure.symantec.com/connect/articles/upgrade-overview-sep-121-release-update-5-121533750...
Feel free to PM me if need any assistance.