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Well ♥♥♥♥. You are right. I ♥♥♥♥♥♥ up for real this time.
When an NPC dies, the game runs a death script - this cannot be undone. The only way to "revive" an NPC that the game has marked as dead is to load a previous save from before the NPC died. While resurrecting with the console may seem to work, the game still sees the NPC as dead, so dialogue, actions, and quests that depend upon that NPC will not run. Also, you should be extremely careful when using console commands, as they can break your game - and if you do use a command, always make a hard save before using the command.
"You should never resurrect any named characters in Skryim. Game runs death scripts for each of them. Using resurrect command does not undo these scripts and there is no known way to reverse them.
Resurrecting character that has death script records in save file usually ends up badly. In best case scenario you get a useless NPC that is not tied to any quest and is cut out of the progress. In worse case scenario you get NPC that is comes constantly more and more bugged, tangling game scripts even further and ends up making a real mess out of your game.
Resurrect is among commands that has been classed as dangerous and should not be used in a game. It is a developer test command and should be treated as such. If you already made a mistake of using that command, then load a save before that." - Ilja
http://steamcommunity.com/app/72850/discussions/0/405692758710158199/#c405692758710646756
Ilja:
"Skyrim runs death scripts to all named characters. Resurrecting them through console does not undo the script. As far as game knows, -character- is dead and remains that way.
Effects for using Resurrect command vary. Some characters may act and talk as usual, but very often - especially with merchants and quest characters - game will get bugged, when it is no longer running scripts to dead characters, but those (as being "resurrected") are trying to cause scripts to run."
http://steamcommunity.com/app/72850/discussions/0/351660338700199057/#c351660338700216175
AND:
"Problems with resurrect have bee documented far and wide in this forum. You will notice the conflict sooner or later, especially if merchant character dies."
http://steamcommunity.com/app/72850/discussions/0/351660338700199057/#c351660338700279973
See also:
http://steamcommunity.com/app/72850/discussions/0/451848854987583992/#c451848855002328904
http://steamcommunity.com/app/72850/discussions/0/451848854985133583/
REGARDING RECYCLEACTOR:
"Recycleactor does refresh the character, but as far as I know, it does not undo death scripts.
I can't see why it would, seeing that it basically just restores the character. That character may be "refreshed", but death scripts and stand-in triggers should still be active." - Ilja
http://steamcommunity.com/app/72850/discussions/0/405692758710158199/#c405692758710784953
EDIT: deleted references to Skyrim mods - didn't think to check forum I was in when posting! (whoops!)
Work your way through the setstages and quest completions commands until you get past the part she has any involvement.
http://fallout.wikia.com/wiki/Liberty_Reprimed
It lists Professor Scara as an alternate but your problem is she somehow died between the first quest and stage 70 of the next quest. So the alternate was never activated.
Now you could try to set Scara as the alternate as well. Try restarting the From Within (the previous quest) and skipping it to stage 70 where you tell Maxim about Li being dead.
http://fallout.wikia.com/wiki/From_Within
Let me know how ya make out.
As for your suggestion, I already tried that before making this post, but resetting and changing the quest stages literally does nothing.
She only has one set of #s, base id 5e63f ref id 61c39 there is no seperate #s listed on the wiki.
So you either need to do one of the following:
1. Reset theLiberty prime quest. High chance it wont work, but dont know til you try it. As long as you got a save point to fall bakc to you really cant ♥♥♥♥ it up any worse.
ResetQuest ae51c
2. Force Scara to become active repalcement for Dr Li. You might be able to take this route since you are technically not repeating a completed stage.
Setstage ae51c 40
3. Use setstage commands to get to a spot you can finish from.
Use this command to find your stage:
GetStage ae51c
Then proceed to follow the flow chart on the wiki page using this command(replacing # with the stage #)
Setstage ae51c #
Eventually you should be able to finish the quest cycling through the stages. Not completing and setting the different stages in the flow (ie using the complete command) can screw up the next quest in the chain.
Also keep in mind AFTER you set a stage you need to reload the area the stage takes place in. Changes will not take effect if you are in the zone. For example, setting stages while inside the Cabot House does nothing. Setting the stage outside THEN entering Cabot House activates the new stage setting. I prefer the setting the stage in a different zone then entering.
EDIT: Speak to professor Scara doesn't work as she doesn't respond. I'll see if I can find a workaround.
EDIT 2: Found a workaround. Setting the stage to 60 skips all her dialoge and I have no started construction of Liberty Prime. Thank you!
So it was the fact you did not reload the zone after setting stage the first time? Ya I forgot to mention that earlier. Kind of an important thing to meniton, lol.
You might run into trouble down the cstage chain? One of the last few stages looks like it had dialogue wiht Li in it.