Using M2ePro with WebInterpret is possible. Yet, a specific feature in M2ePro must be switched off in order to prevent your foreign listings, managed by WebInterpret, from being relisted automatically.
3rd Party Listings Synchronization must be turned off.
It is critical to avoid automated relisting on your foreign items.
This would generate items not handled - and maybe already relisted by WebInterpret and may potentially create policy breaches, and extra fees generation (if it applies).
Please access the configuration page as shown below and set 3rd Party Listings Synchronization to "NO" :
Once this is done, M2ePro will consider you foreign inventory created and handled by WebInterpret as "independent" and will not try to take ownership on it.
For more information, please refer to M2ePro official documentation: http://docs.m2epro.com/display/eBayMagentoV6/Synchronization