Never attribute to malice that which is adequately explained by stupidity.
Absent clear evidence of intent, a court is far more likely to decide that the document was misfiled by mistake rather than as a deliberate act to conceal its existence.
However, that simply begs the question.
PCJ is a common law crime in England and Wales. The elements are an accused:
does an act or series of acts;
which has or have a tendency to pervert; and
which is or are intended to pervert;
the course of public justice.
Further, the course of justice must be in existence at the time of the act(s). The course of justice starts when:
an event has occurred, from which it can reasonably be expected that an investigation will follow; or
investigations which could/might bring proceedings have actually started; or
proceedings have started or are about to start.
So, you are not quite right that the initial misclassification is not PCJ. It depends on what the GP knew or reasonably suspected at the time. If they were aware of an event that might reasonably lead to an investigation then the course of justice has already begun. In any event, knowingly concealing the document in the course of an investigation is PCJ.
However, PCJ is only applicable to actions taken in "public justice" - a dispute between a doctor and a patient is not "public justice" unless and until it has become a matter where the interests of the Crown are involved. For example, once a court case or arbitration has been or is reasonably expected to be initiated. If the parties have agreed to negotiate or mediate their dispute, this is not a public justice matter.