I am using OH 2.5.11 in Docker environment.
As I understood, I have to modify some path in userdata folder (from org.smarthome.openhab2 to org.openhab).
Is there any utility, which would help me with the migration in Docker or do I need to adapt all config files manually?
I am not sure where you saw that. Without seeing your configuration, nobody here can assist. Part of the flexibility of OH is permitting many ways of installing and running. The documentation on Docker Hub mentions some of them.
personally, watchtower (docker container, which can update other containers) did the update for me and just some few things were to do after the update in the thing files but nothing really hard stuff.