Alessandro - the email address policies in E2k7 (like recipient policies in E2k3) chiefly control the primary proxy addresses. Although you can stamp secondary addresses with the RUS, there can be many of these and the RUS will ignore the extras. You can always add/remove secondary addresses without any effect on the policy or the primaries. When you switch from one policy to another policy, the former primaries are retained as seconday addresses to allow mailflow to continue interrupted to these previously existing addresses. This is intentional and by design. The primary effect of the email address policy change would be to change the "reply-to" address exhibited by the mailbox user, not to remove custom or legacy secondary proxies.
If your goal is to completely flush all non-policy proxy addresses from the mailbox, you will want to script this removal-of-secondary-proxies action as part of the cut-over from one policy to the other. The good news is that in Exchange 2007, the new email address policy will be properly applied (for primary proxies) immediately after making any writes to the mailbox user using the Exchange 2007 tools.