Yes it must have, as I posted above. I had it happen with both SD-0 and The First, when they got killed by my group while I had the infinite-loading-screen-of-death. After restarting the game, the bosses counted as killed successfully, but I only received the basic CQ points. So, as you say, any payout on login will be without stronghold bonus. A bug that will likely have been in the game forever, but only coming to a broader surface now.

Second week, and it happened again. Stronghold bonus again doesn't apply to the Galactic Seasons: Progress cq objective. It does auto-complete upon login for subscribers on Fridays, so will be an issue going forward. 6.460 CQ points "lost" at 150% sh bonus. (But won't be an issue for me any longer as my sub runs off next week anyways. So good luck to all subs to get this fixed.)

It looks like it will happen the same with other conquest objectives: I had a very bad week once when I got the infinite loading screen of death when beaming in to SD-0 and The First. So the group started without me. Once I logged back it, I still got the progress for the kill but I had only received the 13k (?) unbuffed conquest points. The objective was completed and the points were just lost. I had never thought about those two things related, but they very likely are now you mention it.

You could have seen your answers from the multiple threads on this topic already. Different people have very different needs for conquest. And no, unlike you claim, I for one don't consider the rewards "not that great". For me, they used to be my reliable income of tech fragments. With 5 toons on lvl80 I could reliably upgrade two legendary implants per week. None who complain about the changes here said that they "hate" conquest, as you claim. The issue is, that the normal activities we do and that should reward us with activity points (aka conquest points) just don't give any or few. So we have to grind stuff we don't necessarily would have to finish the weeklies. It takes understanding that people play the game differently. And this understanding would have made this question unnecessary.

Just want to thank you for doing what OP should have done: breaking his long-winded "oh mighty corpo defense" post into readable paragraphs.

I already lost 16 Fragments due to this. This is a severe bug.