This report is a bit confusing. My knowledge of how vendor contents is evolving between versions of 5.x (and even within each version) is very limited. My apologies.

I've got a dev/testing environment, built from git repositories.
My root folder is a clone from ezpublish-platform
After switching to stable-5.1 branch, I remove vendor, and run composer update.
Once the update completes, I remove vendor/ezsystems/ezpublish-kernel and create a symlink to a clone of ezpublish-kernel repository.
ezpublish-kernel also has stable-5.1 branch selected.
Now, any attempts to run php ezpublish/console.php cache:clear is failing with:

[Symfony\Component\DependencyInjection\Exception\ServiceNotFoundException]
 The service "ezpublish.spi.persistence.cache" has a dependency on a non-existent service "ezpublish.cache_pool.spi.cache.decorator". 

It seems that, composer update is forcing me to have https://github.com/ezsystems/ezpublish-kernel/commit/5aa01c8b36d57eda808cd97b366fa0ab58cf03b9 which has not been merged into 5.1

I also have a bunch of other resources symlinked (basically every resource that has it's own repository) but I do not think those can be related.
I'll gladly provide any additional details that you require