Are converts with a Jewish father (let's say Shmuel) also called ben Avraham (instead of ben Shmuel)?
Is this so, since your gentile descent is kind of wiped out through the act of conversion?
yeshiva.co answers your question (here)
A child born to a non-Jewish mother is non-Jewish regardless to the father's status. Therefore all that applies to a convert applies in this case as well – halachicaly he is not his father's son.
He will be called "Ben Avraham Avinu" – at least for Gett and Ketubah matters. (Piskei Din Yerushalaim)