One of the more unusual aspects of these viruses is their ability to persist in the host, even after apparently being cleared by an effective immune response, which is typically determined by a clearing of symptoms, and not by analysis of the viral "load". The host appears to eliminate the virus by classic immunity, and those infected typically recover without persistent problems. Or at least most apparently do, so far.
However, this persistent, low level viral production seen in some people is similar to what is seen in a primary natural reservoir for coronaviruses, which are bats. They too seems to have low levels of persistent cornavirus production, which does not cause them any apparent harm. But then they would likely have evolved with these "parasitic" infections and have managed to avoid long term health problems. That is why viral "isolates" from bats, and other animals, are suspect in the current pandemic. Of course, humans might not be prepared for this type of viral infection. It remains to be seen,.
Clearance of the virus without ill-effect seems not to be the case in many people, like the "long-haulers' in the above story. Some have been re-assayed for the virus, and it comes back negative. But how close are they looking it? The extent of symptoms strongly suggest this virus is much more than a respiratory threat. It appears to be a threat to nearly every organ and tissue in the body. A good reason for this is its interaction with the receptor(s) involved in neurological functions. and some suspect the ACE* complex as a primary target. These receptors are found on many cells all over the body, but particularly those of the neurological system. The bizarre behavior of brain fog and worse conditions like hallucinations might indicate that a low level of circulating active virions are causing such symptoms, and not everyone is prone to it (yet).
For anyone suffering from these problems, it would be highly advisable to determine if you have retained active production of the virus at low levels, as described above. Such a test would require more work up than the standard genome assay. Careful sample handling and greater amplification of long-hauler blood/tissue samples might provide a clue about the nature of their problems.
Continuous low level virus production could certainly cause damage to many organs if they infect them and cause significant cell death, and localized amplification of the virus. The immune system would like tamp down such an outbreak rather quickly, but if persistent viral production is the cause of extended problems post-infection, additional therapies like antivirals may be required, in addition to boosting immune function, if possible. Some of the soon to be approved (we hope) vaccines might help alleviate symptoms if low-level virus production is involved. They may provide a unique response to suppress viral levels even more.
^ As the lungs are damaged via the virus, all those that were infected will have to build up their lung capacity; this will take quite a long time. Those parts of the lungs that were damaged, may never actually return to normal. These people need to try long breathing techniques and gradual exercise to build up their lung capacity what they have left.