The error "Quantity must be greater than 0" is related to Out Of Stock Feature changes made on eBay recently.
eBay allows revising item QTY to 0 only if the Out Of Stock feature is enabled. The option 'enable Out Of Stock' was moved to global configurations and it seems to be disabled by default.
All sellers who would like to use this feature now should enable it in Site Preferences.
Please, check and enable it to allow revise qty to 0. Once the option is enabled on eBay, please try to revise items via the M2E Pro and check if the error persists.