If the existing user profile will automatically be reused (I didn't think that was possible, good to know) then it sounds like you just have to handle the user assignment in the pool. Sounds like the users won't have to do an additional login for this to take effect, though you'll need to make sure they're not logged in while you change the assignment as an active session for the "old" user will block the new one from logging in through View. vdmadmin won't take a csv file as input so you'd have to run it for each (un)assignmnet, manually finding each user assignment might be a pain, as you say. If you're comfortable scripting and using ldap then the simplest method would be this:
backup your configuration by running vdmexport
ldap connection to localhost, dc=vdi,dc=vmware,dc=int
get all entries under ou=servers (they'll all have GUIDs as names, don't be alarmed), filter by string value of the original user SID on the pae-sidstring attribute
replace pae-sidstring attribute value with a string containing the new user SID for any matching entries