I really have no clue. I checked the triggers again, and I also did various quick tests on the map, but everything works correctly: as soon as the Overlord is seen by one of my units, it loses its invincibility. Also, the Overlord being invincible but the Spores Colonies being normal is something that seems impossible, since their status is managed by the same trigger. I really don't know what could have happened during your playthrough.

It is no big deal. I have removed the concerned triggers on my end and made Orange Zerg turn on Epsilon Squadron once it is defeated.

I'm fine with that, even though that doesn't sound like a good idea: in particularly complex maps, removing a seemingly self-contained trigger might have unexpected consequences on other triggers, causing unpredictable behavior.

I guess I am just not sure I get the intent behind turning an Overlord invincible in the first place.

That's perfectly normal and understandable. I will try to explain it as best as I can.

The Overlord provides sight to the cluster of Spore Colonies (since they are surrounded by cliffs on all sides). The Spore Colonies are meant to discourage the player from attacking the yellow Terrans from the back of their base, taking advantage of the cliffs. As you have surely noticed, the yellow Terrans and the orange Zerg will ignore each other, until the player penetrates the orange base and destroys their Hives, at which point yellow and orange become enemies (they don't start as enemies because yellow would concentrate its effort on destroying orange, thus ignoring the player). However, the yellow Terrans would wipe out the cluster of orange Spore Colonies after the player took possession of the resources in the bottom left corner of the map (amassing a huge number of Wraiths in the process, which was bad). This is the reason why the Overlord and the Spore Colonies remain invincible as long as the player doesn't discover them: to make sure that the Spore Colonies remain intact, thus maintaining their deterrent purpose of discouraging the player from attacking the yellow Terrans from the back.

It's been seven years since I made that map, so I might be forgetting something, but this should sum it up.