THE PURSUIT of the now-you-see-'em, now-you-don't EPA papers has been interesting, and it will be a very good thing if some agreement can now be worked out between Congress and the White House to avoid a Class-A constitutional confrontation. But this has never been the substance of the matter. The confrontation seems to have been in part a result of a mindlessly escalating exchange over accessibility and in part a congressional device to 1) force attention to the policies that have been guiding the agency and 2) break a political stalemate in which neither the agency nor Congress has been able to win any degree of trust or cooperation from the other.

Beyond the struggle for the papers lie the questions about health protection, a point made on the opposite page today. One crucial accusation is beautifully illustrated by a current law suit. The Chemical Manufacturers Association and the Environmental Defense Fund, two natural antagonists, have joined in litigation to force the EPA to collect more and better data on the effects of chemical wastes on health. The chemical industry thinks that more research will prove the dangers to have been overstated; the Environmental Defense Fund thinks the opposite. But they agree that the law requires the EPA to pursue the subject.

One of the Reagan administration's original complaints about the EPA was that many of its rules had no firm scientific basis. That was, and is, true. It is fair to assume that further research will demonstrate that some rules are needlessly tight and can be safely relaxed. But the agency has been cutting back sharply on research and data collection. It has reduced its monitoring to a point at which it is becoming impossible to know whether air quality, to take one example, is getting better or worse.

Who lunched with whom, and whether any federal crimes were committed over the lunch table, are questions on which the administration is going to have to satisfy not only itself but Congress and everybody else. Better sooner than later, but that is secondary. Beyond that, the president is being pressed toward a judgment on the job that the EPA, under its present management, is doing to protect public health.