Snakes carrying nido will test negative some of the time. Beyond the limits of testing (the replications in PCR are not perfectly accurate), RNA viruses are very fragile and don't survive long on the swab (they need to be overnighted to the lab). Most importantly, snakes don't shed the virus consistently. Three consecutive negative tests are the standard for ruling out nido when it is suspected.
Though I'm not very familiar with the details of disease progression and all the related issues with testing, you might also consider testing for paramyxovirus. Something to look into, anyway.
I use RAL for my testing (just sent out nine swabs today on new arrival testing; all my new booids get a boid panel and a crypto panel), and would recommend them. They're respected (not that FH isn't), less expensive, and offer a very large range of pathogen tests.
https://www.vetdna.com/
About the best collection of info on nido I've yet to bump into are these two Snakes and Stogies episodes:
https://soundcloud.com/theherpetocul...dr-porcher-dvm
https://soundcloud.com/theherpetocul...d-steve-tillis
Those were originally linked in this recent thread:
https://ball-pythons.net/forums/show...ight=nidovirus
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