Complex sentence: Vlašić had been under investigation for "dubious doctrine, the manipulation of consciences, suspect mysticism and disobedience towards legitimately issued orders" and accused also of sexual immorality with a nun, which he had covered up.
Split into simpler sentences: Vlašić had been under investigation for "dubious doctrine, the manipulation of consciences, suspect mysticism and disobedience towards legitimately issued orders". He was also accused of sexual immorality with a nun which he had covered up.