I recorded this video while trying it, might help visualize it (should be what you described).
https://youtu.be/3jMfRkt1Yyo

Should work, did you try to load a savegame from scenario 2, from before proceeding to scenario 3?

It must be from before the 3rd scenario, otherwise it will just load the old file.

Yes, you probably need to restart the scenario for the fix to take work. Since when you save, the issue is saved into the savefile.
If it still does not work after restarting the scenario, please report back. Also welcome to confirm if it works

This is a known issue, and has been the focus of latest test builds.
It seems to be fixed in the current one. At least for me, unsure of others yet.

<r> Baloogan has something on his site on Offensive ECM. Perhaps something there:<br/>
<URL url="http://baloogancampaign.com/command-documentation/offensive-ecm/"><LINK_TEXT text="http://baloogancampaign.com/command-doc ... nsive-ecm/">http://baloogancampaign.com/command-documentation/offensive-ecm ...

<r> As I understand it:<br/>
<br/>
<B><s>[b]</s>Joker Fuel<e>[/b]</e></B> is a preplanned fuel state (Not always used), that is reached before bingo fuel state.<br/>
Can mean many things, incl:<br/>
"no more afterburner"<br/>
"no more gunnery event"<br/>
"prepare to stop mission advisory"<br ...

the system default browser

+1
Definitely would like this. Until then, I tend to right click, copy URL and then paste it in my default browser.

Will be nice to see you stream again I should hopefully be able to make it.

I am from and live in Faroe Islands...

Yep, that seems have fixed it...
Now I can check examine doctrine, without stuff changing. And only options that I change are actually changed.

Seems to work as intended now, but I'll keep and eye on it for a while still though.

<r> This one only seems to happen if I change the refuel doctrine, which seems to change both settings. <br/>
The training scenario, oddly works differently. If I don't open the doctrine window, nothing happens. But as soon as I open it, it changes "Engage opportunity targets" to yes.<br/>
<br ...

I have reported the bug.
It is also in B470.

<t> Just found out how to reproduce this every time in B469, all scenarios it seems.<br/>
"Operation Bass Drum" as an example.<br/>
<br/>
* Start scenario.<br/>
* Go into "Doctrine & ROE" in Game menu.<br/>
* Expand "Use Refuel/Unrep" and select "No"<br/>
* This instantly sets "Engage ...

Route for the rest of the aircraft attached:

<t> I also did it much more aggressive first couple of times I tried this.<br/>
I only sent the B-2 bombers that way. Refueled them over Oman. Then sent them stealthily along the Iranian/Pakistani border quickly north to Afghanistan (with fingers crossed), and then to Bagram.<br/>
<br/>
For ...

<t> Here's a short on how I did it.<br/>
<br/>
I made the decision to work out from Bagram AB, since it's nice and close.<br/>
So the first 24 hours was all about armin/readying assets, and relocating to where I wanted them.<br/>
<br/>
I decided to use the B-2 bombers for the task, so I started ...

No, you need to take out that bunker and TELs that the rebels have control over.
But if you only take out the bunker, and leave any TELs alive. Then they will launch a nuclear missile. Which is basically what you are meant to prevent.

<t> Just beat this one myself, without making anyone hostile except the rebels themselves and a couple of airfields nearby.<br/>
This was a difficult one for me, I'm not hugely experienced.<br/>
Advice: Patience.<br/>
Plan far ahead and rearm and relocate assets to where they may be needed.<br ...