There are basically only two reasons why orders are imported twice.
The cleanup at Clean up shop import orders table is set too short (tab Cleanup in Administration > System > Basic Settings)
The project in the shop importer has been changed and the check mark for multi-project shop has not been set.
Multi-project shop: In this shop, products from different projects are offered. This is a special function.
You only need this option if you offer products from different projects in your shop.
Example: Your shop offers some products that require a different logistics process or that require a special customer check (e.g. requesting a trade register excerpt) directly after the order is placed. These products can be purchased together in this way. However, after picking up the orders to xentral, different processes are triggered (e.g. different email templates, customer check is required, different logistics process, different invoice sending, different stationery etc.).
See also Online Shops - Order import settings.