Order number suffixing and sequencing

When you edit an order, by default, Edit Order will append a suffix to the order number for the new version of the order to indicate that this is latest version of the order. For example, if you edit Order #1001, Edit Order will create Order #1001A with your updates.

Because of the way Shopify works under the hood, this can give the impression that orders are not being created in sequential order.

When Edit Order suffixes an order number from say #1001 to #1001A, Shopify still increments its internal counter under the hood, causing the next order placed on your store to have "skipped" a number.
For example, if you have an order, Order #1001, and then you edit that order. The order number slot that "would have been" Order #1002 ends up getting used by the edited version as Order #1001A. When you receive the next order from a new customer, the order will get assigned Order #1003.
So because of Shopify's internal counter, you'll end up with the following order number sequence:
#1001
#1001A
#1003
This gives the impression that number #1002 has been "skipped" or is "missing". However, under the hood, #1001A is just taking up #1002's slot.

The good news is that this is a normal (albeit, confusing) behavior of Shopify when an order is edited and does not represent any orders that went missing. Though we can't stop Shopify from incrementing their internal counter, fortunately, we haven't heard of any merchants about issues that this causes, especially once they get used to it.