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When I removed the drain bolt, fluid was very dark but only about a liter or less came out. That was first uh-oh moment.
So after draining, I put 2.5 L in the dipstick hole, run the engine for 15 sec and checked the dipstick. fluid level was nowhere near minimum level. Second uh-oh moment.
At that point, I figured the fluid was really low and not changed for long time and put 0.5L more and it overflowed. After cleaning mess, I ran the engine for another 15 sec and checked the fluid level to see the level being in middle.
I added 0.1L more just to be sure, and wrapped up.

I will drain and fill again soon, but even after the fluid change I can still feel the slip from 2nd to 3rd- and 1st gear shifting at 3K RPM now. It shifted 2.5K RPM with same level of acc. applied. Should I be worried?

 
Rep Power: 221

Do 3 drain and fills in a row with a 10 min drive in between each to get the fluid warm and engage all the gears. It's possible that the trans has permanent damage from being run with low fluid for a long period of time. Try the 3 drain and fills first, fluid is cheap.

 
Rep Power: 209

Which ATF fluid did you use? After the 3x3 drain + fill Colin suggested you may want to try this as a last effort if there is still a shifting issue:

 
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I was thinking doing once more next week, do you think I should expedite?

I’m using Valvoline Maxlife. Maybe I’ll add this on 3rd fill when there’s still slips.

 
Rep Power: 209

If it's not shifting properly after a 3x3 drain and fill then there's most likely internal damage. It wouldn't hurt to try the lubegard additive as a last resort but keep your expectations low.

 
Rep Power: 221

The way I described is how to do it according to the factory repair manual, except they would run it on a lift.

 
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I'll try driving a bit more this week, maybe the ECU is confused from ATF back in normal level?

But how likely will my transmission fail, like being stuck in gear? A bit of slip is fine for me considering it's done 384K Km now.

 
Rep Power: 221

thats wishful thinking....

Need to do the 3x drain and fill to see, you might get lucky

 
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Done 2nd drain and fill, slip is reduced. Might be better on 3rd...?

 
Rep Power: 221

Certainly worth trying for the $30 in fluid