Swapping Domains - Could this be a problem?

I have an eccomerce site that has been hit by Penguin( we'll call this "site A"). My plan is to build a new mini site (already done - Call this "site B" it has the same directory structure as site A ) I plan to kill site A for a few days and request deindexing in WMT for the whole site. Once it is out of the index I plan to switch the domains around so my old eccomerce store is ranking again but obviously with a new domain name. My original domain will be be used for the mini site I built and left on the back burner for now.

Could this cause issues with duplicate content? The reason I plan to do it this way is that im still not sure if site A will come back at some stage and I don't want to go to the trouble of building a new eccomerce store with all new content.

You might have duplicate content problems from switching the content as Google does remember old content even if it has been deindexed. Redirecting site A to B may or may not pass on the penalty. BTW, i would recommend to try to deoptimise site A with raw url and 'click here' like links while building up your site B and doing your link building carefully. It is alot easier to rank new sites like your site B than to recover penalized ones especially given the gap left by all the previously top 10 sites now penalized. Best case scenario long term...you have two sites ranking well.

Yeah I think you are jumping the gun a bit. I am seeing a bit of a recovery in the sites I have that were hit by penguin.

In theory what you are doing will work but you are going to be doing a bit of starting over. I don't agree with the duplicate content issue mentioned above and the reason why: Press releases get indexed on a lot of different URL's and they are duplicate content and I run a lot of real estate sites and the listings on my all my sites get indexed and they are duplicate content across all the sites I have and there is no penalty.

I also see tons of ecommerce sites selling the same products using the same sales pages and they don't get clobbered.

Everyone thinks duplicate content is a source of a penalty when Google ranks that content based on which page it feels is the best to display but you still see identical sales pages in results either higher or lower.

Give your site another month or two and build some good links to it and see what happens.