Sounds like you have a good idea on what where and how.hello; Forgive me if this has already been covered. I have been lurking on this thread but may have forgotten some of the information.
One point about bb and substrate. That there is now no substrate does not also mean there are no bb on surfaces of a tank. It is my understanding the bb can and do colonize many surfaces even in bare bottom tanks. Pretty much any surface where there is some flow.
On the nitrite test results. Others have speculated on what conditions might promote zero ammonia and at the same time some level of nitrite. My comments will be about using the test kit. As others have suggested clean the vials and use distilled water.
One other suggestion is to run the tests on some distilled water. The pH should be neutral and all other readings should approach null. Best I can recall this was a method I used back in the 1970's as a "standard" to calibrate water test results.
Some have mentioned RO water and I did use a lab that made their own RO water. Best I can recall the chemist told me it can be used in place of distilled water. Please feel free to correct these assumptions if I have this wrong.
Distilled is "cleaner" than ro, ro still has some impurities depending on the filter system. The closest to pure nothingness is distilled or ro/di.
But that is a great idea to test the test. Not sure either if op has done that. But that sounds like a pretty serious test if it goes down that far.

