Is it possible to run backward annotation (sync changes made in pcb to schematic) from command line, e. g. using kicad-cli? I have read the kicad-cli documentation and found nothing.
Are there specific thing you want in this back annotation?
KiCad does have: PCB Editor / Tools / Update Schematic from PCB, and this can change footprint links in the schematic. Maybe it can do more too, but I don’t know further details.
I know about the PCB Editor / Tools / Update Schematic from PCB. I want tu run exactly this from command line, not by clicking in kicad itself.
I am using KiVar to define and switch assembly variants. I am also using KiBot to automatically generate fabrication data. I have design with several assembly variants and I wat to generate automatically fabrication data for all of them. So my idea was to use kibot-cli to set the assembly variant and then run kibot to generate the data.
Problem is, that assembly variant switching by kivar tooks place only in pcb and changes are not synced back to schematic. Sch and pcb are not in sync, when I run kibot, which results in unpredictable kibot behavior (some outputs match schematic, some match pcb and the results are not consistent).
It is possible to fix this problem by running Update Schematic from PCB, but it must be done manually, by opening the kicad project and clicking to it. I want to do that from command line, as a part of script. I know that kicad has command line interface, so I expected to run something like kicad-cli --backannotate <schema> <board> but it seems, that such command does not exist.
It would have been a bit quicker if you wrote that in your first post. It also looks like a valid & logical feature request. If you want to make a feature request for this, then open an issue for it on gitlab.
I would urge you to reread the original post and title 
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Sometimes stuff are implemented, but not documented I was thinking, that it may be already there, but I just was not able to find it.
I also read somewhere, that KiBot somehow emulate mouse clicks and key strokes to achieve things, that are not accesible via kicad-cli. This looks like possible solution for this, but I can not implement it on myself. Maybe someone can help me or have some idea?