Please guide me what to do with this message and avoid the big mess:)
How to just change these parts?
This may not be right as I’m still new to KiCAD and learning my way around, but it sounds like in your schematic there are symbols with duplicate references.
I opened up a project I have, copied a symbol, and pasted it making sure it had the same value in the “Reference” field in symbol properties. If “CA1A”, “TL1B”, etc. are references, if you update their values to be unique on the board it should go away. Here’s an image of what I was talking about for reference:
And just to clarify on this, it’s not complaining about the “1757284”, it’s complaining about “J5” being the same. 1757284 is in the “Value” field and not the “Reference” field, and it seems to be ok with those being the same.
Hope I got this right!
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When you experience an annonation mess and you are beyond the point that you cannot Ctrl Z your way out of your mess. You may be best off by annonating things by hand. You can do so in either the schematic or the board design. Be lucky it are just 5 components. I once had meself a much nastier situation 
Re-annonating the design may even make it worse.
General advice, after a board update, check if the annonation is still OK and if needed use the mighty Ctrl Z in both PCB as schematic editor.
Best of luck to you 
Bas
- Make a backup of the project in the current state (maybe save a backup that is already in your backup folder too.
- Start experimenting with the settings in that dialog you opened. Also read some manuals.
- Then when you get stuck, read How To Ask Questions The Smart Way
- Then ask a new question, or post a follow up question in this thread.
@jurek
To update a PCB, every symbol needs a unique “Ref”.
Correctly annotating a schematic means giving each symbol a unique Ref.
In your case, you annotated, but you ticked the box “Keep existing annotations”. Kicad annotated, but found 5 items with duplicated “Refs” and couldn’t change them automatically because you told it not to.
This box is used if you particularly wish to keep some annotations. This action is really asking Kicad to check for and list any problems.
You now need to locate these items listed and change the Refs to something different and not currently
in use.
Alternatively, if you tick “Reset existing annotations”, Kicad will re-annotate the whole schematic in one of the two “orders” available.
Of course! two 1757284s is no different to having two 1K resistors on a schematic. 
Yes 
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And this comes the chaos 
No, I don’t want that.
Yes, I see, that’s the best solution right now. Thanks.
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That is why you are offered the choice. 
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