I cleared both old Black Temple and timewalking Black Temple, only the old lockout is displayed in SavedInstances while both are displayed in Blizzard's lockout list.

Here's the return from GetSavedInstanceInfo():

[1]="Black Temple",
[2]=238126822,
[3]=132307,
[4]=33,
[5]=true,
[6]=false,
[7]=524353537,
[8]=true,
[9]=30,
[10]="Timewalking",
[11]=9,
[12]=9,
[13]=true

Here's a screenshot of Blizzard's lockouts:

And a screenshot of SavedInstances: