You may want to contact RICOH to see if there is an official answer. The method of using the “factory reset” is a bit cumbersome. Putting into developer mode used to void the warranty and stil might.
If you delete the files with the API (like the mobile app), it should update the database inside the camera.
If you delete with a USB cable with the camera mounted as a filesystem, you may have problems. I had problems with the numbering in my tests.
The THETA X has a reset item on the menu of the body of the camera. This may accomplish what you want. I have not tried it.