So I had to change the leaky evaporator and for that of course I had to disconnect the negative terminal of the battery. According to the manual, you have to perform initialization after you disconnect the battery. Here is the procedure for ISC learning -

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PERFORM INITIALIZATION (SFI SYSTEM)
(a) Apply the parking brake and chock the vehicle.
(b) Connect the intelligent tester to the DLC3.
(c) Put the engine in the inspection mode (See page
ES-34).
(d) Select the following menu items: DIAGNOSIS /
ENHANCED OBD II / DATA LIST / PRIMARY /
COOLANT TEMP.
(e) Warm up the engine with the A/C switch off until the
coolant temperature becomes 83°C (181°F) or
more.
(f) Select the following menu items: DIAGNOSIS /
OBD/MOBD / HV ECU / DATA LIST / SOC.
(g) Move the shift lever to the N position, set the A/C
switch to MAX cool or turn on the front defroster,
and leave the vehicle until the SOC value becomes
below 40%.
HINT:
If the SOC is substantially below 40%, the auxiliary
battery may go dead. Therefore, do not allow the
SOC to reach substantially below 40%.
(h) Move the shift lever to the P position and turn the
power switch off.
(i) Disconnect the negative terminal from the auxiliary
battery and leave it for 1 minute or more.
(j) Reconnect the negative terminal to the auxiliary
battery and turn the power switch on (IG).
(k) Select the following menu items: DIAGNOSIS /
ENHANCED OBD II / DATA LIST / PRIMARY /
COOLANT TEMP.
Check that the engine coolant temperature is 83°C
(181°F) or more.
HINT:
If the engine coolant temperature is below 83°C
(181°F), start the engine by depressing the
accelerator pedal with the shift lever in the P
position to increase the coolant temperature.
(m) Select the following menu items: DIAGNOSIS /
ENHANCED OBDII / DATA LIST / PRIMARY /
CALCLOAD.

Move the shift lever to the D position while
depressing the brake pedal with your left foot.
(o) Depress the accelerator pedal with your right foot
while firmly depressing the brake pedal with your left
foot, and maintain an engine load value of 45% or
more (60 to 70% of full acceleration) for
approximately 30 seconds.
NOTICE:
Do not perform this step for 40 seconds or
more.
(p) Shift the shift lever to the P position. Turn the power
switch off and then wait for 5 seconds before putting
the vehicle into the READY-on state again.
(q) Select the following menu items: DIAGNOSIS /
ENHANCED OBD II / DATA LIST / USER DATA /
ISC LEARNING.
(r) Check that the air conditioner is off. Lightly depress
the accelerator pedal and release it when the
engine starts.
(s) Check that "COMPLETE" is displayed on the
intelligent tester screen.
HINT:
• If "ISC LEARNING" is not completed within 1
minute, repeat steps (o) through (r).
• The engine will usually stop when "ISC
LEARNING" is completed. However, the engine
will not stop even when "ISC LEARNING" is
completed in such cases when the charge level
of the auxiliary battery is decreased.
-----------------------------------------------------------------------------------

I have problems doing the bolded above. In (g) I discharge the battery and the state of charge shows below 40 (actually 35 or so) and then I perform the next step which is to disconnect the negative terminal. After that when I turn the power ON state of charge goes above 50! The battery is relatively new as I bought it from Toyota about 18 months ago. Anyway, I proceed to the next step, and finally, when I am doing step (o) I cannot get calculate the load around 50%. It either stays in the 30s and when I floor the accelerator (does not change in between) it jumps to 85% or so. I am using techstream. I was able to complete it but I am not satisfied it's done right as the load was never correct. ISC learning value was 4.76L/s (I am guessing this is airflow needed for the idling when the engine is warm). If I read some numbers here (GSIC - Global Service Information Center) it might still be high. Has anyone done that? Thanks in advance.

 

When you disconnect the 12V, it clears out the battery state data. The ~57% is the "default". The next time it starts, it evaluates the battery's voltage response to current and recomputes the SoC.

I've disconnected Toyota hybrid 12V hundreds of times and never once done the above procedure with no effects. The car figures everything out from normal driving.

 

Thanks for the battery explanation. This makes sense.

I want to do this procedure correctly as after I removed the battery (actually twice as I forgot to connect one connector and I had to pull the dash again) I could hear a metallic ticking sound (not only going uphill but pretty much anywhere) and it was much louder so much that even my wife said looks like dash is not sealing right and the car is much noisier now. After ISC learning that reduced drastically and it's not too bad now probably like before. Just wanted to see if I could make it better by doing it correctly.

 

Any luck? I have a high idle and the isc learning value is 4.21 l/s.

From techstream

 

Sorry No. Mine is higher; it has changed a bit but still higher than yours. Did you disconnect the battery?