That's important information. It counters theories that ME is due to gut or microbiome dysfunction. Gut and microbiome dysfunction can certainly worsen ME symptoms, but if flushing out the digestive tract doesn't stop or at least reduce the symptoms significantly, it's not likely to be the root cause.
Flushing out all the material in your digestive system with the shankhaprakshalana yoga technique would not remove bacterial biofilms attached to the intestinal lining; it probably would not even flush out loose bacteria that are attached to the lining.
After all, you can have a bladder infection on the bladder lining, even though the bladder is constantly being flushed out with the urine that collects there.
That's not to mention L-form bacteria, where a bacterium changes its morphology so that it can live inside human cells. Most bacterial species are capable of converting into the L-form state, and this strategy of hiding inside host cells protects them from much of the immune response, and from antibiotics.
Furthermore, you can get what is known as bacterial translocation, where whole bacteria actually pass through the intestinal lining, and start to work their way inside the body. Such translocated bacteria may live in the lymph nodes attached to the intestines (mesenteric lymph nodes), and these bacteria can also migrate into the liver, spleen, etc.
Once these translocated bacteria have entered the body, they may also start forming biofilms or L-form infections in the organs they infect, to protect them from the immune response, and from antibiotics.
Factors that promote bacterial translocation across the intestinal lining include a leaky gut and deficiencies in the immune response. Chronic viral infections of the intestine are known to cause both. Dysbiosis is another factor which can promote translocation.
So in this way, a persistent viral infection of the intestinal lining (as Dr John Chia has found in ME/CFS patients) could set up the conditions where you get increased bacterial translocation, increased biofilm formation or increased L-form bacteria in and around the intestines.