Hi Vicky,
Very interesting question. I can understand why you were given the original advice; the PPG is (IMHO) questionable here - if you're doing a brand new plan you're not just changing the extent or approach of existing policies but putting in place new ones that will have different application; the old map is entirely superseded (as are the old policies in the previous plan) so showing changes to it is wrongheaded. (To pour even more scorn, policies maps don't really "illustrate geographically the policies in the Local Plan" as the NPPG states - they illustrate certain areas that specific policies apply to. If you were to illustrate every single policy in your local plan your policies map would be a heady mess; how on earth would you illustrate a policy excluding backland development from residential gardens?)
Still, I think you're right that you need to do this, as the PPG should be followed. I agree that your layer-by-layer suggestion is probably the best way. Take a simple example, where the old and new policy approach is similar - town centre boundaries for example; you could simply show the old and new boundaries, or just show the changes with a dotted line or whatever. If it's more significant policy shift then you might want to make this clear by 'deleting' the previous entry on the policies map and putting the new approach as a new entry. You'll probably need some sort of commentary to describe what's happening.
We haven't yet done this for a full new Local Plan, but we did recently do a partial review which involved changes to the policies map; you can find the relevant document here. It's not perfect - I think it would have been helpful for there to be a commentary describing what's being changed.
In short, I don't think there's a straightforward way to do this. Sorry!
Rob
