At the time he accused her, he was reeling from Kristen's assault. He later apologized once he realized his mistake. Daniel NEVER apologized to Nicole for his treatment of her and in his usual smug, satisfied way, felt that everything he did was right and Nicole was wrong.
Only towards the end before they became engaged, did he suddenly decide they should be together and just got together with her, but there was no onscreen resolution of the issues that existed between them. I want Nicole to have a baby but not with Daniel who treated her terribly.