I think this lack of missions happens when the alert is over. Today, after the weekly tick, missions will probably appear in new alert systems, but possibly also in other, human controlled or recovery systems.
But anyway, I still think it's a bug, because if an alert is finished in one system, it doesn't mean that the whole war is over, so that all missions disappear!
Today we will probably get some new CG, so for a while all players will forget about the current problems, so then some bugs will be patched in 16.01, but only some. Then the excitement about the U17 will start, and that's how the poverty continues.
Usually you can find them in systems without Alerts so long as they are within 20 LY of the system with occupied military settlements.
As indicated by the mention of on foot terminals.
I'll be doing a check later myself, hopefully things should be back to previous state of affairs.
Felix is right on the money. I've been doing these missions for weeks now, and the system you get the mission from doesn't have to be in Alert. It just needs to be within 20 ly of the Thargoid controlled (and possibly invasion state, though never found those) state.
The systems I listed in my previous post (both target system and systems giving missions) aren't the first set I've done. I moved there after the last system I used to visit was recovered by humanity and taken off the table.
HIP 19198 is firmly under Thargoid control. It hasn't even come close to crossing the 33% line where all the progress won't reset.
I prefer to take missions FROM a system in Alert state, as that should help both systems. The only difference in taking the missions in an Alert/Invaded system vs. a normal system is the former requires you to take the missions in your ship under the "Operations" section of the mission board. If in a normal system, you can still find some of the AX restoration missions in that section of the ship mission board, and those choices - plus a few more, on occasion - from the Support section of the On-Foot terminal mission board.
Post update 16 - None of these missions were present. There wasn't a system state change, but those missions are just GONE.
I will check again, when I get home tonight, to see if the server tick had any effect. My suspicion is that they accidentally borked the mission board system. I searched that blasted Issue tracker of theirs and someone had already posted an issue stating that all the missions they were doing (non AX) from Robigo were missing from their mission boards once 16 dropped, so this may be related to more mission types than simply AX Restoration. It clearly isn't ALL missions, as I still saw plenty of normal missions on both boards.
If I confirm the issue, I'll add it to that other guy's ticket, since it's probably related. And then I'm out. I am FED UP with having to find, document, and report their bugs and then watch the issue expire in their issue tracker.