Reinstalling EMS Server

HI All

Does anyone have a procedure on how to do this, just been having so many issues with the software. I feel like i just need to start over again. 

Do i need to remove the agent from all the endpoints first, or can they be left alone (current version of v6.4.1 is missing over 60 endpoints), just not pulling them through from AD, even though the AD enumeration is working).

Also numerous endpoints showing different configurations to what is displayed on the EMS Console