I am a computer programmer at a world famous secular hospital. I work on the hospital’s Electronic Patient Record system. The major feature of this system is the documentation of patient encounters: operative notes, discharge summaries, clinic notes, etc.
As you can imagine, there are all sorts of things in these notes that go against the teachings of the Catholic Church, including abortions, illicit fertility treatments, contraception, etc., etc., etc.
Still, there is no moral dilemma because the fact of a patient’s abortion is a fact. The abortion did not occur because it is documented in the system. The birth control wasn’t prescribed or used because it was documented in the system.
And the fact that a person is on birth control is a relevant medical fact that physicians who treat the patient need to know so that they don’t do something else to harm them.
No, there is absolutely no cooperation in evil going on here, simply by documenting what has already occurred.
From a moral perspective, it is no different than an epidemiologist studying a potential link between abortion and breast cancer. The facts are the facts. Documenting them is actually a testimony to the Truth, and is therefore a morally positive thing.