I am a British Citizen immigrating to Australia.
I have to provide police clearance from any countries which I visited for more than 3 months.
I worked in Portugal For a few summers between 2006-2009, I no longer have the Identity Card from there, which I only applied for in 2008 and never used.
How do I get a police clearance without it?
If I don't put my stays in Portugal on my Oz visa app will they check?

Help Brain Melting!

I would have to say, just don't mention that part and don't put it on the app. You wouldn't get police clearance without it anyway.