Merging two shops into one is not easy. Prestools provides a tool to merge the orders of one shop into those of another. Not only the order records but also the customer records and their addresses will be merged. This is a complicated operation as those orders, customers and addresses need to get new id's as their old id's are already occupied in the new shop. Prestools has fully automated this procedure.
Whether the customers can keep their password depends on the question whether those shops have the same Rijndael keys. If not, customers will need to reset their password.