In cases where the simples are not correctly assigned to the configurable, you can manually attach them by first going to the product in the Admin Panel and confirming how many variations should be attached to the product.
In our example, there are 20 variations
The next step is to go to the backend of Magento and look at the product. In this case, you can find the product and see that only 2 simples are attached.
Here we can see that the 5.5M and the 5,5W are the only two attached. So we have to find the other 18 variations in Magento, then delete them and then reset them in the Modern Retail Admin panel so that they go back over to Magento and attach correctly.
To do this, you need to search Magento for the other simple products. In our example , you can see that the attached 2 simples actually have two different names so we have to search both. Searching by the first reveals 10 simples and searching by the second shows 7.
In both instances, you need to select and delete all the simples EXCEPT the ones that are already attached correctly ( the 5.5M and 5.5W)
In this unique case, even after searching the two names only 17 simples were found and three were still missing. (They had a third name)
So the missing three had to be found using the integration ID (highlighted in blue) to find in Magento. Once they were found, they were deleted too.
Once the simples have been deleted, you will have to wait for the next QTY REPORT job to run , which will recognize the items as deleted and mark them as such in the admin panel. Once you see them in the admin panel as deleted, you can use the RESTORE ALL button to reset them and then they will go back over to magento and attach correctly to the configurable product.
After you hit the Restore All button, the simples will be sent over to Magento when the next NEW PRODUCTS job runs. You should then see all the simples attached to the configurable.