For so far unknown reason it is possible to unload specific gates in TP HD by just loading a different specific gate into the console's memory.
So far only one gate connection was figured out: The two gates in the western and eastern wings of Lakebed Temple are connected to the big gate before Aeralfos' room in City in the Sky.
This leads to a significant timesaver in most routes that saves around 45 seconds and skips three rooms in CitS, making it even shorter than before.
1) Head to Deku Toad in Lakebed and grab the small key in the chest you use to get on the railing
2) Long jump over railing, blow up rock, kill Deku Toad
3) Get Clawshot and head back to main room
4) Go right to stairs and clawshot to upper floor using the vines
5) Enter East Wing to load the gate
6) Progress through the game normally
7) Enter Fan room in CitS
8) LJA across and leave through north door
9) Gate is unloaded - go down to Aeralfos