Sometimes I move the handles on top of the node that they are from but then I can’t select them again to get them out because it just selects the node. What do I do?
Select any mode nearby and use the Tab/Shift+Tab key to move the selection to the hidden node.
Or, select the segment (with both handles) and click a button in the Fit Curve panel (shortcuts ctrl-opt-1 to 8).
Why do you move individual handles on top of nodes in the first place?