I have such directories structure on server 1:
I've found the reason. As for me - it wasn't clear that Rsync works in this way.
So correct command (for company1 directory only) must be:
rsync -avzn --list-only --include 'company1/' --include 'company1/unique_folder1/***' --exclude '*' -e ssh user@server.com:/path/to/old/data/ /path/to/new/data
I.e. we need include each parent company directory. And of course we cannot write manually all these company directories in the command line, so we save the list into the file and use it.
1.Generate include file on server 1, so its content will be (I've used ls and awk):
+ company1/
+ company1/unique_folder1/***
...
+ companyN/
+ companyN/unique_folder1/***
2.Copy include.txt to server 2 and use such command:
rsync -avzn \
--list-only \
--include-from '/path/to/new/include.txt' \
--exclude '*' \
-e ssh user@server.com:/path/to/old/data/ \
/path/to/new/data