You can find below  the most common issues that can cause this problem :

• Out of stock mode has only been enabled in the module, but not on eBay.
  In that case when the module will try to update a product with zero quantity, eBay will provide an error that the quantity is invalid.
  You need to activate the out of stock option on eBay as well, you can do this through your “My eBay” account preferences.
• You are launching a manual sync with the “UPDATE ALL PRODUCTS” mode  and not “UPDATE OUT OF STOCK PRODUCTS”.
  The “Sync” menu have a dedicated synchronization type meant to update zero-quantity products only.
  If you want the zero-quantity products to be included also in the global update sync, you must act in the “minimum quantity filter” in the general options of the module, making sure that in the general options of the module, taking care to set it to 0 (zero) and not 1 (default).