Questions are great, I'll do my best to answer them!
What you're referring to is usually found on EGL or similar quality certificates. Quite frankly, the value on the certificate is meaningless. It's essentially a way for the retailer to say look, it's valued at $4,000 on the certificate and I'm giving you a deal at $2,000. The true value of the diamond is $2,000 (for example) and that's what you should pay.
Unfortunately you see this a lot with chain stores as a way to give you a perceived deal or sale price.
It's really a shame this happens as I feel it cheapens Canadian diamonds as a whole.