The Quanta article is talking about something different from what I was describing.

What I was describing is a consequence of the way Paxlovid works: it doesn't "kill" the virus or get your immune system to kill it, it just stops the last step of virus assembly inside cells by inhibiting the enzyme, protease, that catalyzes that step. So while you are taking Paxlovid the virus can still go through all the stages of getting inside cells (the normal way, not the different way described in the Quanta article--each virus particle just infects one cell and does all of its replication there), replicating its RNA there, and expressing all of the proteins that form a complete virus particle along with the RNA; it just can't do the very last step, assembling all of those pieces into more complete virus particles, while the protease inhibitor from Paxlovid is present. But once you stop Paxlovid, the protease inhibitor goes away and all of those virus pieces can now assemble (each set of pieces inside a single cell) to become full virus particles that can infect more cells.

The issue might be that, how long do you have to keep taking Paxlovid before those partially complete viruses degrade enough to not be able to reassemble after you stop.

Yes, and I don't think anyone knows an exact answer to that question, but I think it's been established that the answer is "significantly longer than the current 5 days that a course of Paxlovid is for".