Pending Amazon orders aren't brought into ChannelAdvisor until the pending status clears. This article discusses the ChannelAdvisor and Acctivate options to ensure these orders aren't skipped.
Acctivate integrates with the web store ChannelAdvisor, which can act as a web platform that consolidates orders and inventory quantities for other web shopping carts such as Amazon. Acctivate will import in orders from ChannelAdvisor based on the ordered date and time timestamp. This can be problematic for Amazon orders which are in a pending status because they do not import into ChannelAdvisor until they are no longer in a pending status. The amount of time it takes for the Amazon order to no longer be in a Pending order status can vary, but by the time it's out of the pending order status, the web store template in Acctivate may be looking for orders more recent and therefore the previously pending Amazon order might be skipped.
In order to avoid this situation, it is recommended to allow pending orders (and their quantities) to import into ChannelAdvisor immediately. Then, Acctivate will find these orders during the standard web store sync, but skip them due to their pending status. When Acctivate skips an order, it will put the skipped orders in the Web Store tab of the Business Alerts window. The web store template can be configured to automatically try to resync these with every web store sync, so when the Amazon orders are no longer pending, they will be brought into Acctivate.
In order to configure ChannelAdvisor to bring in pending Amazon orders, you should follow this article.