these are my change notes so might help you with your WEM upgrade ive done multiple like this and never had a issue

We need to upgrade the Citrix WEM infrastructure to the latest CR version 2009 from 1912CU1 to fix a few issues that we have seen in production with the version that we are currently on 1912CU1 this has been recommended as a potential fix by Citrix for the issues we have been experiencing with the WEM agent and high CPU usage. The procces i will use is below 0 Upgrade Citrix license server xxxxx.xxx prior to Citrix WEM upgrade / Snapshot server at hypervisor prior to upgrade and take backup of .LIC files and make sure CSS dates are current 1 Create a snapshot of WEM Broker server at the hypervisor level 2 Backup the Citrix WEM DB on SQL instance xxxx.xxx database name XD_PROD_WEM 3 Elevate SQL permissions to sysadmin temporarily during the upgrade as database upgrade is required or use infrastructure services account which has DB_owner perms on the XD_PROD_WEM DB 4 Snapshot/document current settings in Citrix WEM infrastrcture services config utility 5 In place Upgrade the Citrix WEM infrastructure services server to Version 2009 6 Run the Citrix WEM Database management utility and upgrade Database 7 Upgrade the Citrix WEM Administration console to 2009 8 Re run the Citrix WEM infrastrcture services config utility and confirm setting have stuck if not re enter them from details from step 4 9 Upgrade WEM agents on any PVS/MCS Master images WEM cache will need to be removed and refreshed using Agentcacheutility -refreshcache a ngen update will also need to be run before finalizing and shutting down and sealing the master images