I started the war part and I'm very confused.

[Shaidon]

1st let me tell my story, you can skip it.

Spoiler: Story

I choose Spectacle Island to build the Lupe's Outpost, cause I didn't want to mess with the other 2. What bothered me, since I spend a lot of time building that settlement to support the HQ, and the outpost plan didn't even touched the area that I used. But oh well, I can deal with that. Then Salvador ask for location to build an the military outpost, what could be again at Spectacle Island, but I wasn't sure if was a good idea, so I choose Jamaica Plain. He also suggested to be near the HQ. I want to make an clone army, so I used other mod to create the settlers to send them to fulfill his quest (conscript). All 7, plus a special one that I send first to Jamaica Plain, before I started the mission to convert it to an outpost. Meanwhile Egret Tour Marina got conquered by the Gunners, and that pissed me off, since I was taking care of building that place as well. But seem that was part of the quest, so I deal with it, expecting things to go back to normal after it. First, I had to reload a save, since Salvator continue to attack the settlement defenses and settlers, since they were all aggro, and I couldn't talk to him. Second attempt I manage to deal with it, by baiting most of them outside the ETM, and killing the last two inside it. Managed to talk to him, but the settlement still seems unchanged. Marked as an outpost, the extra flag still there, but changed, settlers still want to punch my face. I left the area to see if that would fix it. I continue his quest to attack the overpass of the Gunners. BTW, all my conscripts where not in Jamaica Plains, but a bunch of Freedom Fighters.

Now for my actual doubts:
1 - How can I get rid of the Freedom Fighters? I turned off the auto hire, what seem that make a bunch of them leave, but my 1st outpost still have only them. I can't kill them, only send them to another outpost, and that is not ideal. I want Jamaica Plains to have only my custom conscripted settlers there.
2 - How can I summon back my conscripts to Jamaica Plains? I checked the war table I couldnt find any option like that. Seem that I need to talk to each one, but I don't even know there they are.
3 - How to change a location back to be a settlement? ETM still marked as and outpost, what changed the buildings there. For now I only want Jamaica Plains to be the official one. Again, didn't saw an option at the table. I found an option Change Settlement Type, want turn into Change Command Post, then give me the two options of ETM and JP, so I choose ETM, but nothing happens.
4 - that first outpost requested by Lupe can be turn back into a settlement? Do I need the structures there for any reason to not break quests?

 

[Antoine Soverie]

How can I get rid of the Freedom Fighters? I turned off the auto hire, what seem that make a bunch of them leave, but my 1st outpost still have only them. I can't kill them, only send them to another outpost, and that is not ideal. I want Jamaica Plains to have only my custom conscripted settlers there.

If you're really against freedom fighters, you can make an outpost at some location you'll never visit (like coastal cottage for example) and send them there iirc. Don't think you ever get new freedom fighters, only generic soldier recruit (might want to turn outpost auto recruitment off as well if you don't want that).

How can I summon back my conscripts to Jamaica Plains? I checked the war table I couldnt find any option like that. Seem that I need to talk to each one, but I don't even know there they are.

You can use the town meeting gavel to summon everyone who's assigned to an outpost (guards, warriors, settlers etc). And/or go workshop mode and move them from one outpost to the other.
If you dismantle an outpost from the war planner's desk (turn it back into a settlement or disown it), everyone in it will leave and you get a prompt for what other outpost they go to. You can't do this with your command center, have to pick another command center from the war desk first. In this case it's likely Jamaica Plains for you. Or ETM since you changed that.
Outposts don't support other types of plots like commercial, farms, industrial - you can change that in holotape options, but do it in advance, before everything is changed to martial.
The "outpost" used by Lupe is not actually an outpost until you make it one (barely anything changes as it's mostly martial residential and municipal plots). If you don't want the city plan you can go back and select manual building and just build whatever the quest wants (all plots separately). Or I guess you could make whatever you built into a layout and apply it later? Think it needs to be a "differential layout", or maybe just pick "don't scrap anything" when you apply it to a settlement already with the city plan in it. Still, you'll need to allow for other types of plots in outposts.

 

[Shaidon]

I not against Freedom Fighters, I just didn't want them on that 1st outpost. I was looking for a way to remove them from the game, and hire new ones if I so desire.
ETM became an outpost without my choice, because was conquered by Gunners while I was doing the quest to build the first military outpost. I was expecting to be something temporary, but after I advanced more into the quest I saw that wasn't the case. The only way to turn that back to a settlement was to set another war table there, and increase the settlement size, since was already maxed. The number of settlers was already reduced there for some reason, I had more than 9. 3 of them was the conscripts that I had to talk to one by one to change them to guard Jamaica Plains, so they will return. Using the gavel was not calling any of the conscripts back. Also returning ETM to a settlement and asking to send people to Jamaica Plain, didn't not send the settlers that was original there. For some reason they disappeared. Only one was labeled as a Settler, I know for sure that wasn't there before. People just vanished, no dead bodies.
It was annoying to see ETM becoming a dead town with plots changed. I changed the options now, hoping won't happen again. Moved settlers from another settlement to fill the gaps.

Oh, and as I said, there wasn't any option at the War Table to actually call all the conscript back to Jamaica. I had to find them on ETM and the other location that I had to use the flare, and talk to one by one. Figure out that changing them to guard would send them back, so I could manage them there. I was confuse cause there was too much with little explanation happening.

I made a layout of my original Spectacle Island, the file was generated at the proper folder, although when I 1st tested, the game said there wasn't any layout saved. Anyway, I just wasn't sure if was OK to change the settlement back again, and mess with some quest.

 

[Antoine Soverie]

didn't not send the settlers that was original there. For some reason they disappeared. Only one was labeled as a Settler, I know for sure that wasn't there before. People just vanished, no dead bodies.

At least some of them will likely be in your capital city if they're not there, if you talked to Charlotte (quest you get from war planner desk inbox) and picked one. If you didn't, it's probably "the main quest settlement" or Stodge's settlement or the most built up one? Whatever place that got a few extra settlers after the assault.

I made a layout of my original Spectacle Island, the file was generated at the proper folder, although when I 1st tested, the game said there wasn't any layout saved. Anyway, I just wasn't sure if was OK to change the settlement back again, and mess with some quest.

Yeah for layouts to be able to be used, they need to be a mod that you have. So you get that log you exported, throw it into the layout maker (https://www.simsettlements.com/tools/layoutcreator.php) and install the mod you got from it. Can be like 10 of them in one esp (though it gets annoying to update it)

Anyway, I just wasn't sure if was OK to change the settlement back again, and mess with some quest.

After Resurgence it's not used in any quests, unless you want it as an outpost for later (for assaulting places in that region). You might want it for that, pretty much until ch3 ends.

ETM became an outpost without my choice, because was conquered by Gunners while I was doing the quest to build the first military outpost. I was expecting to be something temporary, but after I advanced more into the quest I saw that wasn't the case.

It's a good place for an outpost, though it's a good place to have a normal settlement too, so yeah. I'd suggest Sommerville and Jamaica if you do turn ETM back to a settlement.

 

[Shaidon]

Thanks!
I got to make the layout work with the builder with no issues. Interesting that you get to allow adding the layout buildings, while still keeping the previous ones. Although I thought would be best to ask to scrap everything before buiding. Only had a minor issue, with 2 ofthe same 1x1 martial hi-tech, that one had double banner poles, and the other had a bugged pole that wasn't accepting the power cable. Easy fix.

And yes, the missing ETM settlers where all at Sanctuary that I set as the capital long time ago. I had t move them somewhere else, since I did some changes around the triagle of death some time ago, by reducing the number of settlers and structures. I wasn't bothering to look back there again, that is why I missed the increase of population.

Now I need to find a way to move settlers to full settlements (max 20) without affecting the others. I think I need two more at Spectacle, but I going to check again.

 

[Antoine Soverie]

Now I need to find a way to move settlers to full settlements (max 20) without affecting the others.

Since I just ran into this exact roadblock - you can use

player.setav charisma 50

to give yourself 50 charisma and bump your "move settlers" limit to 60 without chems or clothes. I'd just make sure to use it again with your previous charisma level or

player.setav charisma 10

after you're done , or make sure "limit settlers by beds" in WSFW is active.
Edit: yeah just revert it when you're done, that's the best bet or you'll get way too many settlers.