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Dear Customer Service,
I would like to advise, I have a Victron Balancer connected to the 24V system with 2x 200Ah LiFePo4 batteries in serial connection. First three days it was perfectly balanced with a maximum deviation of 1%, but for some reason, the deviation started to be much higher, actually at 5%. What can be the reason? and what can I do? Can I charge this battery with this deviation with IP22 Victron smart charger 24V-16A up to the top? Thank you for your advice.
You would need to charge them both up either individually or you could charge both of them connected as 12v together through the whole bulk absorption float.
Then you can re set them up as 24v system.
Beef up the interlink in the 24v syst as well.
What is your battery voltage (at 24V)?
The balancer is only working during charging and if the voltage is higher than 27.2V.
Thank you for your response. So if I understand you correctly, only during the charging is the voltage higher than 27.2V and during the charging the batteries should to balance tensions? 
Just look at the datasheet/manual:
https://www.victronenergy.com/upload/documents/Manual-Battery-Balancer-EN.pdf
The normal idle voltage of a LiFePO4 battery is around 13,2-13,3V (26,4-26,6V) -> the balancer is OFF.
Your voltage needs to be at last 27,3V (I had a typo there above).
I believe the battery balancer only works at 27.3 volts and above. I would disconnect the batteries, connect them in parallel to each other with no load, let them sit for 24 hours to allow their voltages to equalise, and then connect them back into your system. Now charge them, as you only have a 24v charger and wait till the battery monitor leds light up. Hopefully it will be a green one. It could show under or over voltage on one of the batteries, if so complete the charge and allow the battery balancer to do it's work before putting any sort of load on them.
You need to make sure your batteries are connected with busbars and equal length cabling otherwise you will get ever increasing voltage deviations from the midpoint as they discharge. They should also ideally be the same battery type and manufacture.
Looks like you're trying to get 12V and 24V from the batteries, which is why they're going out of balance. (there's a different load on each battery and a connection to the mid point which looks heavier than just something for the balancer). You must only take a 24V feed from them. If you need 12V, then install a 24/12 Orion converter which will give you 12V without putting the batteries out of balance.
Also the batteries are at different temperatures.
@klaudiagyogyfiova the battery displaying the lower current is the 1 with the highest SOC. Nonsense unless the batteries started discharging with a 5% SOC difference between them.
The fact that both batteries display different current means the SOC will never be accurate for 1 battery.
What sort of BMS's do those batteries have? The battery balancer will balance the batteries, not the individual cells in each battery. The different discharge rates in a series connection could be down to cell imbalance or individual cell internal resistance. Doing what I suggested earlier would probably help you determine if you have a bad BMS or bad battery.
Thank you for everybody's response, so what can be the solution? Is the Victron balancer even working properly on the 24V system? I mean keep in balance not only when it's charging but also when discharging (it's turning only on when the charging is above 95%)
Your battery SOC indicators may not be accurate. One says 50% and one says 55% but there is a 0.2v difference between them. That is not much a deviation.
There seems to be different internal resistances in the batteries them selves that cause different amounts of power to be drawn from each.
Have you tried increasing the size of the battery interlink?
