I'm currently hunting around for a solution to the same problem.
We use something called Tradebox to keep our eBay and Amazon shops synced with our accounting software. So I'm looking to sync Tradebox with Woocommerce.
I've found this plug in: http://www.woothemes.com/products/ordercustomer-csv-export/ for exporting orders and stock details from WC, but I can't find any way of bulk updating stock levels from Tradebox into WC.
I asked Woothemes support if the "Product CSV Import Suite" plugin would help do this job and this is the response I got:
Yeah the Product CSV Import Suite works but isn't completely automated like you would like it to be. There are a couple possible solutions:
1. BrightPearl. I've (me personally, not woothemes) been thinking about developing a BrightPearl extension which is made for multichannel e-commerce solutions. Would you be interested in it if I did make it?
2. You could develop a custom solution. I know you can do remote calls with WordPress' XML-RPC and I know WC 2.1 will include a better API but that's still in development and even when it's done there would have to be custom development on your end.
I've haven't tested the CVS exporter yet. Please let me know if you find a good solution to this problem. :)