Weird Nikon D850 folder structuer with SD and XQD cards

Hello Nikon colleagues,

I use a Nikon D850 for aerial survey. The camera has two card slots, SD and XQD. The camera was set to overfill and the SD slot to be primary.

Recently after the aircraft landed, I noticed to my horror that instead of having multiple folders of 5000 pictures each, the folder numbers are random.

Attached are the lists of the folder in both cards at the end of that flight. Typically if there are 5000 pictures per folder, then there are fewer folders.

Below is a summary of the number of pictures per folder. As can be seen in the table above, the number of images in each folder seems random instead of being 5000.

Perhaps proof that it is not an issue with the SD card alone is also weird XQD behavior:

1. The QXD card is also showing a similar behavior: there should be 5000 pictures in the first folder, and the next folder some number of images based on the remaining space in the card.

2. Based on my previous experience, the folder naming in the XQD should be increasing 129D850, and 130D850 and not 129D850 and 115D850. And at the moment I have conflicting evidence regarding the correct capturing order.

While I am still investigating this, inconsistent imaging order makes geotagging a challenge, as well I am worried about possible missing files. 

At the moment I am unaware that I have done anything wrong with the camera settings. Has anyone else experienced something like this before? Or have ideas how to get to the bottom of this?

thanks