Hi Scott,
Anything you do via EVPM overrules what you have set in the GUI, without reflecting EVPM-settings in the GUI.
I don't believe you can combine the two policies (as a user can only have 1 policy assigned), but you could look into the following:
1 policy
Archive with shortcuts mail older than 3 months.
Delete shortucts when they are older than 12 months
If that is not an option, you might first have to run archving to archive anything over 12 months without leaving shortcuts. When that is done, but you will never know exactly without additional monitoring, you could change the policy to archive everything older than 3 months with shortcuts.
You have to take into account that shortcut expiry is based on creation date of the SHORTCUT! ie you archive now everything older than 12 months with shortcuts, then these shortcuts expire july 2011. What you could do then (coming to mind while typing ;-)) is the following:
Archive everything older than 12 months without shortcuts
Have that run for 2 weeks (to be sure all your mailboxes have been archived)
Change policy to Archive everything older than 3 months with shortcuts, and shortcut expiry set to 12 months.
The last line will make sure that shortcuts disappear when they are older than 12 months.
Regards. Gertjan