Sorry for the delay in reply.
1. In the last episode of the original series, did Rick Hunter's expeditionary
forces actually return or was it just mentioned they were about to?
Yes, they returned. Like in Shadow Chronicles, we see General Reinhardt and Sparks at their SDF-4 post in scenes that virtually mirror what we see in this movie, though the other REF soldiers are offscreen (much as the rest of Scott's resistance team are here). While Rick's a prominent offscreen character all through out New Gen, we don't actually see him until Shadow Chronicles. This is followed up in my next response.
2. In the last episode of the original series, were the Invid and Reflex Point
not destroyed by the resistance fighters because in the Shadow Chronicles
they are still on Earth and still seem to be at full strength?
You should know, the events of The New Generation's last two episodes run concurrently with The Shadow Chronicles' first half-hour, 34 minutes to be exact. The Invid were never destroyed, in both The New Generation's last episode and Shadow Chronicles, they leave the Earth. Because of the concurrent nature between the separate mediums, the majority perspective in the last two episodes is from Scott's resistance team while Shadow Chronicles is from the REF's.
3. Why do the Children of the Shadow want to destroy all beings who use
Protoculture?
As "Marlene"/Ariel explains, "Because they fear its awesome power". That's all we got so far.
4. Is there any continuation of this storyline in either film or print?
Not as of yet, though a continuation known as Shadow Rising is in production. There is prequel-esque material that paves the way for Shadow Chronicles, outside of the core series. The "OAV" (original animation video) movie Robotech II: The Sentinels features the REF's departure from Earth in 2022, providing an epilogue piece to the surviving Macross Saga characters while bridging to the Masters story and foreshadowing New Gen. It also introduces main characters in Shadow Chronicles like Vince Grant, his wife Jean, and Janice (albeit in a different form). The canon comic mini-series "Prelude to the Shadow Chronicles" is set roughly 20 years later, leading right up to the plot in The Shadow Chronicles and provides a few story transitions between The Sentinels and Shadow Chronicles; whereas the Sentinels feature show how the REF's journey began, Prelude shows how it concludes.
Any Buffyverse comic that's post-"Not Fade Away" is non-canon, my PoV says. Denny Crane!
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