"City of Light" (http://db.hellfire-tbc.com/?quest=10211) is the quest that triggers the possibility to chose between Aldor and Scryer once you have completed it and turned it in.
When choosing one of these quests you should get friendly with the faction you choose and get hated with the other faction. When you then do more and more quests for the faction you choose your reputation for that faction increases and the repuation for the other faction should decrease (if it can decrease any further). Besides that every quest you do for one of the factions Aldor/Scryer should also give you Sha'tar reputation.
But what happens is that you will get unfriendly with the Sha'tar, which leads to not being able to talk to any Sha'tar vendor (for example the badge vendor).
Your reputation to Sha'tar should not be touched by completing one of these quests.
"City of Light" (http://db.hellfire-tbc.com/?quest=10211) is the quest that triggers the possibility to chose between Aldor and Scryer once you have completed it and turned it in.
After that you can choose between two quests from Khadgar: Allegiance to the Aldor (http://db.hellfire-tbc.com/?quest=10551) Allegiance to the Scryers (http://db.hellfire-tbc.com/?quest=10552)
When choosing one of these quests you should get friendly with the faction you choose and get hated with the other faction. When you then do more and more quests for the faction you choose your reputation for that faction increases and the repuation for the other faction should decrease (if it can decrease any further). Besides that every quest you do for one of the factions Aldor/Scryer should also give you Sha'tar reputation.
But what happens is that you will get unfriendly with the Sha'tar, which leads to not being able to talk to any Sha'tar vendor (for example the badge vendor). Your reputation to Sha'tar should not be touched by completing one of these quests.
This is what happened right after turning in the faction quests: https://i.imgur.com/dB6DXNR.png (Scryer Quest) https://i.imgur.com/6UNJFwK.png (Aldor Quest)