my wifes co. just told her a new law in ca makes them pay for nor taking a lunch she never singed anything about taking or not she worked there for 3 years without a lunch break and always took it at her desk while still working do they have to pay for the 3 years?

There are two different issues here.

If she worked through her lunch period (whether approved or unapproved), then she must be paid for that time. This is not new; it's been part of the federal Fair Labor Standards Act forever. For that, she can file a claim for unpaid wages with the Division of Labor Standards Enforcement.

And there is a penalty (with limited exceptions, which don't appear to apply here) of one hour's wages payable to the employee if a meal period that is required by law is not provided.

It appears the company was clueless before, and are now trying to get thing right, at least somewhat, by requiring that she take her lunch period. Just for information's sake, was she asked to work through? Did her supervisor or manager know she was working through her lunch?