I agree with Peter that the obvious answer is simply to file the 5500-SF for the applicable years as soon as possible. The delinquent filer fee is capped at a very reasonable amount.
If, for some reason, that is not an option, you might also consider:
PPA sec. 1103 amended the definition of "one-participant plan" to include a plan that covers only 2% shareholders in an S-corporation, including attribution. This change was not reflected in the instructions to the 5500-EZ until the 2020 plan year (as Jakyasar noted). If the entity sponsoring the plan is an S-corp, and the years in question do not predate the effective date of sec. 1103 of PPA, then the plan sponsor, if they found themselves under investigation by the government, might claim that they were interpreting the definition of "one-participant plan" under the changes made by PPA.
If the plan sponsor decided at some point not to allow the son to participate in the plan, they might have memorialized that decision somehow, possibly by a formal resolution, or a note scribbled on a cocktail napkin, or something in between. Depending on the circumstances, that could have the effect of closing the plan to new entrants, including the son. If the plan was later restated but without the participation freeze, you might see if it would be possible (for example, under EPCRS) to retroactively amend the plan to conform it to operation.