Hello,
Yes, as Chetan suggested simply update the clients via Auto-Upgrade Feature.
Migrating from Symantec Endpoint Protection v.11.x clients to Install Symantec Endpoint Protection v.12.1.RU1 could migrate flawlessly without any issues.
Yes, you migration should be in the manner below:
SEPM 11.x --->> SEPM 12.1 RU1 ----->> SEPM 12.1 RU1 MP1
It is always recommended to perform a Disaster Recovery for SEPM 11.x before Migrating to SEP 12.1 as a Backup step.
Here are few steps to look at for Migration:
1) How to upgrade the Symantec Endpoint Protection Manager (SEPM) to Version 12.1 RU1
http://www.symantec.com/docs/TECH176260
2) a) Upgrading or migrating to Symantec Endpoint Protection 12.1.1000 (RU1)
http://www.symantec.com/business/support/index?page=content&id=TECH174545
b) Upgrading or migrating to Symantec Endpoint Protection 12.1.1101 (RU1 MP1)
http://www.symantec.com/business/support/index?page=content&id=TECH187753
3) Steps to prepare computers to install Symantec Endpoint Protection 12.1 client
http://www.symantec.com/docs/TECH163112
4) Activating your Symantec Endpoint Protection 12.1 product license
http://www.symantec.com/business/support/index?page=content&id=TECH162623
Also, check the Articles for the Migration on :
Quick Access to Symantec Knowledgebase Articles of Symantec Endpoint Protection 12.1
https://www-secure.symantec.com/connect/articles/quick-access-symantec-knowledgebase-articles-symantec-endpoint-protection-121
SEP 11.x to SEP 12.1 Upgrade process graphical overview
https://www-secure.symantec.com/connect/articles/sep-11x-sep-121-upgrade-process-graphical-overview
WhitePaper for Migration: https://www-secure.symantec.com/connect/downloads/migration-whitepaper-symantec-endpoint-protection-version-121
Hope that helps!!