Node on the maps

I been destroying the nodes the energy pod that go up and down, but the icon still on the maps, is that right or am I missing something.

Guide here: Guide: "FNIX Rising" side missions

Based on your description, look for “7. Energy Independence.”

I have only one side mission with the upside down chevron “Never Trust Anyone” which is completed showing all ticked.

You talk about “nodes on the map”. Are these “nodes” the red/white hexagonal ones as seen on my map?:

If so, these are POI icons, showing locations of FNIX structures and they do not disappear from the map.

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Thank you for that, if you don’t keep a record of which ones destroyed, you can tell from the icons.

FNIX generators respawn. Only those that are specifically targeted in Energy Independence mission, remain destroyed for forever (redacted inside the ground, without ever going up).