I completed a DNA test through Ancestry. One match was with an IVF donor concieved family member  who I have now made contact with.
Her father  wants his details to remain private.
From information she has given me, I can identify two brothers, one of whom is likely to have been the persons father. 
I am anxious to protect the anonimity of the father but would like to note the existance of the donor concieved child and her two siblings who share the same father.
I have made a private note  against both brothers, protected with square brackets.
Any further advice on how to record this link would be welcome.

It sounds as if you have identified the father by "jig-saw" identification (putting together the pieces).  If you make enough of those pieces public others will be able to identify the father by jig-saw identification.

If you want to "protect the anonymity of the father", I would keep all the pieces outside your tree, the conceived child, the circumstances of their conception, the two brothers and possibly the two siblings (because if you record them it opens the question as to why their (IVF conceived) sibling is not showing). It will just be an undocumented and hence invisible branch of your tree.

In genealogy there is no obligation to record all information! My late mother (who was adopted) has her genetic lines documented outside the family tree, because her paternal family I think have no knowledge of her existence (or of course the circumstances by which she was conceived). I have made the decision to effectively leave two of my six grand-parents out of my family tree.

It's not worth the risk of causing very grave offence.