*spoilers*

In Dragonfall, is there a way to sucessfully protect the flux state from invasion in the end?

I have only managed to save half of it, walled off, after an attack.

I killed APEX and released the dragon.

I may be mistaken, but there's no ending (expect the bad one) that contradicts the already established Shadowrun canon. It is, after all, a sprawling series of TTRPG that's at the 5th edition - and with number of novels to boot. Somehow, I doubt that going against that (slow failure of the F-state with the complete eradication of anarchist-controlled part of Berlin further in the future) was ever in the cards for HBS.

Actually, there is. If you leave APEX alive and allow it to control the Dragon, it effectively negotiates a ceasefire/truce with SaaderKrupp/word-tasting-dragon-dude (can't believe I can't remember his name, but I'm sure you know exactly who I mean).

I guess APEX threatens to sic Feurschwinge (possibly with enhanced features and/or virus, since it's continued to research it) on any Dragon that wants to invade, but doesn't want to expand, so everyone just chills at the existing borders.

The flux state definitely still exists in this ending, though I can't recall if it still gets split prior to the negotiation between AI and dragon - I think it doesn't since the invasion doesn't start (?).

It's probably not a great situation though, since APEX interprets the flux state as allowing total anarchy, but at the same time does whatever it takes to preserve it at all costs (which tends to include "disappearing" anyone who gets too close to the truth, apart from you and your team). So you have an enforced anarchic state merged with a shadow police state - you're free to do whatever you want, as long as this doesn't involve attempting to discover who's actually running the show. And since it's "enforced anarchy" it's probably still chaotic gang warfare in most of the flux state, since APEX makes no attempt at any kind of internal control not directly related to preservation of the state.

Naturally, this is far removed from the canon - though not the furthest removed from canon of the possible endings...

Hansel.

Ah yes Hans Brackhaus (Lofwyr's human form).

Have you played any of the UGC by Cirion (seberin, on Gog) ?
Especially in CalFree in Chains (which I am currently playing through again), but elsewhere too, Hans makes a cameo and is roundly insulted. :)

edit: gremlin attacked my post adding typographical error, so I added a convenient link, to the wiki, all about Hans.

Yes, Seberin's UGCs are awesome (IMO better than most of the official stuff). So far I've only played through the Antumbra series (I believe he makes a cameo near the end of that one), but haven't played the other two he's released since (CalFree in Chains or the one prior to that) - which reminds me, that's something I need to get to!

From what I recall from end of Antumbra, you end up fighting him if I recall...

I prefer not to reveal the end of Antumbra, but you many be correct. :-"
Play the sequels (The Caldecott Caper, first) in the third engine (HK). The Caldecott Caper is my favourite mod; I think it only just loses out to Dragonfall.
It's much better than the port of the first game into the third engine (DMS: Vox Populi), although Ryan Swank ("Wave.of.Atla") gives a masterclass in Matrix design in that. ^_^
I'm just about to complete CalFree in Chains again, too.