Background: There is no way to visit all 3 of Stone Sea, Burning Library, and Blade Grave. The game only lets you choose two. This is my workaround for rebel path. I chose Forgebound, Unbroken, and Sages and this guide intends to get you the Earthshaker quest

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Workaround (Updated 2018-02-03)
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After reading the conversation files, it seems like the global variable tracking # of factions in alliance is the key. This should involve the minimum amount of changes to achieve what we need and likely being a generic fix for all factions. 

Consequence: The solution appears to be work, however, it will mark as one of the previous quest lines as failed. Notably, the one you already did and showing up in dialogue in Step 5. This only impacts ending cut-scene.

Steps:
1. Click ~ to open console
2. Click enter
3. Enter the following line by line
Iroll20s
setglobalvalue FQ_RB_FactionsInAlliance 2
4. Go to Ascension Hall and start conversation
5. Select the route you haven't done yet - MAKE SURE  YOU DON'T SELECT THE ONE YOU ALREADY DID

Re-enable achievement:
1. Open your savegame with 7-zip
2. Extract MobileObjects.save
3. Edit your MobileObjects.save in Notepad++
4. Search for m_disableAchievements
5. In the line below, change to:
<Simple type="System.Boolean, mscorlib" value="False" /> 
6. Put MobileObjects.save back into the save as above
7. Load your save and enjoy!

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Workaround (Updated 2018-02-02) [Deprecated]
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A workaround inspired by lukasm568. Try at own risk, since it may break the Chrous invasion

1. Go to Tyranny game folder
2. Go to Data/data/design/conversations/factionquestlines/rebel
3. Back up fq_rb_arris_rebelpath_fourthmeeting.conversation
4, Rename fq_rb_arris_rebelpath_fourthmeeting.conversation to fq_rb_arris_rebelpath_fifthmeeting.conversation
5. Clone fq_rb_arris_rebelpath_thirdmeeting.conversation and rename to fq_rb_arris_rebelpath_fourthmeeting.conversation
6. Identify the faction leader (XXX) you want to recruit (e.g. hundredblood for StoneStalker, Renato for Sages) and edit fq_rb_cv_XXX_ascensionhall.conversation (backup first)
7. Look for the XML FlowChartNode of "Assets/Data/Design/Conversations/FactionQuestLines/Rebel/FQ_RB_Arris_RebelPath_FourthMeeting.conversation", clone that entire node, and put it right after the original one
8. In the new node, change  Assets/Data/Design/Conversations/FactionQuestLines/Rebel/FQ_RB_Arris_RebelPath_FourthMeeting.conversation Assets/Data/Design/Conversations/FactionQuestLines/Rebel/FQ_RB_Arris_RebelPath_FifthMeeting.conversation
(ii) Also in the same node, change the "3" that is two lines below "FQ_RB_FactionsInAlliance"  to a "4"
[still writing this guide]

Now, we are going to fix dialogue strings
9. Go to Tyranny game folder's Data\data\exported\localized\en\text\conversations\factionquestlines\rebel
10. Back up fq_rb_arris_rebelpath_fourthmeeting.stringtable
11. Rename fq_rb_arris_rebelpath_fourthmeeting.stringtable to fq_rb_arris_rebelpath_fifthmeeting.stringtable
12. Go inside fq_rb_arris_rebelpath_fifthmeeting.stringtable and replace all occurrences of "fourthmeeting" with "fifthmeeting"
13. Clone fq_rb_arris_rebelpath_thirdmeeting.stringtable and rename to fq_rb_arris_rebelpath_fourthmeeting.stringtable
14. Go inside fq_rb_arris_rebelpath_fourthmeeting.stringtable and replace all occurrences of "thirdmeeting" with "fourthmeeting"
[Still writing. Need to check if this breaks the Chorus invasion afterwards]

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Older Workaround (No longer work with latest?)
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Warning: This disable achievements until your re-enable them (see below)

1. Click ~ to open console
2. Click enter
3. Enter the following line by line
Iroll20s
setglobalvalue FQ_RB_UnlikelyAllies_QuestFlow 1
setglobalvalue FQ_ES_STATE 1
startquest fq_rb_qst_stonesea
areatransition AR_0502_Halfgate South1

Note: the areatransition command does not actually unlock the area but rather is a onetime transit to it. If you want to unlock it, there are two ways:
A. Unlock all maps in console - This is undesired as it unlocks everything but if you don't mind the enter the command in console:
unlockallmaps

B. Edit save game - This is tedious but is permanent. At the same time, if you want to re-enable achievements, then you need to edit the file anyway. Instructions below

1. Save your game after you enter Stone Sea and the quest started
2. Find your save inside: C:\Users\User\Saved Games\Tyranny
3. Download and install 7-zip
4. Download and install Notepad++
5. Right click save file -> 7z -> Open Archive
6. Drag MobileObjects.save to your Desktop and open with Notepad++
7. Search for "VisibilityType". There should be only 1 result. Under "Items" in the line below, you will see a tonne of <Simple value="..." /> lines
8. Go to the 62nd of the <Simple value="..." /> lines. It should read <Simple value="Hidden" />. Change it to <Simple value="Unlocked" />. Note: Counting this gigantic list is very error prone. If I am wrong, then to unlock the 61st or 63rd line
9. Save the file
10. Right click save file -> 7z -> Open Archive
11. Drag the file into your 7-zip window
12. Load your save and enjoy!

Re-enable achievement:
1. Edit your MobileObjects.save as above
2. Search for m_disableAchievements
3. In the line below, change to:
<Simple type="System.Boolean, mscorlib" value="False" />
4. Put MobileObjects.save back into the save as above
5. Load your save and enjoy!