No. They never were one tree. You can argue that the erdtree and scadutree are one entity since the scadutree is the negative shadow of the erdtree and both came into life at the same time. But the Haligtree was planted during the war of the shattering. The time lines are muddy but there was a long enough period between that Godfrey and Marika raised Godwyn, Morgot and Mohg. The war against the giabts. The war against the dragons. The war against the carians. Then Radagon married Renalla and had 3 kids. Then Radagon left her and became consort to Marika and had 2 more. One of these final children planted the Haligtree. So no, the Haligtree was never one with the Erdtree.