Noob question on 48v battery repair

balance the cells so that the voltage on all cells is the same and the problem goes away

It is a 12S pack and should be between 50.4 V and ~ 42V. You may want to try correcting the balance by using a single cell charger to bring the low groups up to match the higher ones.
I worry about the safety of this battery, considering that some cells have been replaced the quality of the rest may be questionable. If you do try to rebalance, please do it outside and closely monitor the procedure.
EDIT: I went back and took a closer look at the photos and realized I was wrong. It is a 13S 5P battery. The question is, where is the missing voltage?

I thought that charging protection board also balances the cels...

I have this charger for RC models: https://www.aliexpress.com/item/32800729065.html?spm=a2g0o.productlist.0.0.428078eazvRAuM&algo_pvid=null&algo_expid=null&btsid=0bb0623116158278077206652e97ae&ws_ab_test=searchweb0_0,searchweb201602_,searchweb201603_

This charger can charge 6 cells, but these groups have more than that.. can i charge single group of these 18650 with this charger?

Now another question appeared ... original cells are 2000mah, the ones i put as replacements are 3400mah... will that effect the usability?

if you started to change the rest, the battery will constantly unbalance, and then use IMAX and align the cells to the same voltage

Daltonjr said:

I thought that charging protection board also balances the cels...

I have this charger for RC models: https://www.aliexpress.com/item/32800729065.html?spm=a2g0o.productlist.0.0.428078eazvRAuM&algo_pvid=null&algo_expid=null&btsid=0bb0623116158278077206652e97ae&ws_ab_test=searchweb0_0,searchweb201602_,searchweb201603_

This charger can charge 6 cells, but these groups have more than that.. can i charge single group of these 18650 with this charger?

Click to expand...

You would need to set the charger to 1S, and charge at a low rate (e.g. 1A) through the balance leads for the particular cell group.

Daltonjr said:

I heve measured the voltage on that battery controller wires, and i get these values:

1st wire is ground - 0v
3,65V
7,77 4,12v
11,88. 4,11v
15,99 4,11v
20,00 4,01v
24,20 4,19v
28,30 4,10v
32,10. 3,80v
36,00. 4,10v
40,10. 4,10v
44,30. 4,20v
48,00. 3,70v

Click to expand...

You are missing one cell voltage. Your battery looks like a 13S5P. There must be 13 cell voltages. You have only 12. You need to measure the output of the pack. It should be around 52V. The cell voltage of the last one is missing.

I think you need to pump the brakes, put down the soldering iron and chargers, supply more information and wait for feedback. Right now, it looks like you've taken all the right steps to eventually burn your house down. Visually, counting the cells, it looks like a 13S5P pack, but your other info points to 12S.

"i have this battery which is 48v and i think its 13s."
TBD, since it appears to be connected to provide 12S
"I found bunch of dead cells and replaced them."
Dangerous move for a noob and even the experienced need to be careful
"original cells are 2000mah, the ones i put as replacements are 3400mah... will that effect the usability?"
Big mistake
"As this is 48v battery pack, i suppose it should be around 54,6v when fully charged, but mine shows only little above 48V."
Sounds like a recipe for a battery fire, if you're charging a pack electrically connected as 12S with a 13S charger.
"Looks like 3 parts are not charged. I assume that means that controller is also bad.."
Not charging evenly because of the mismatched cells.
"But still if all batteries were charged i would get still around 4,5v too low. Like one battery "pack" is missing.."
Yes, that's the issue

"What am i missing? What should i check?"
Provide as much information about your main charger and battery (links, pics of the label, specs, etc.), the old cells, the new cells, and what you've done so far, and wait for advice on next steps. You should also go to the battery subforum and read the stickies on battery building. Don't pick up the soldering iron and plug in the battery and charger before you know what your next steps are.

Thank you all for the input. I decided i will return this to my friend and advised him to give this to a proffesional who knows that stuff. I shouldnt mess with this in the first place, because i almost made a fire with shorting diy spot welder.

Stay safe, thank you.