We are looking to place product across various marketplaces, but for internal reasons cannot keep these items active on our main site. Will the inventory for these items update in Magento even if they are disabled? Unfortunately we have not sold any of these types of SKU's in our marketplaces, and are looking at software that will pull our inventory direct from Magento. Version is 220.127.116.11
The simple answer is yes.
Assuming you are using the standard Magento Import/Export (API will work as well), if you are sending product data for products that are disabled in Magento, they will still update.