I successfully created a jenkins task with Git SCM checking out a git repository with some git sub modules include. (I use git client plugin V 2.0.0, with advanced submodules behaviors - "Recursively update submodules" - checked and "Update tracking submodules to tip of branch" - checked ). Job gets build successfully. Later on I removed some sub modules from the list, for example:

git submodule deinit some-project
git rm some-project
git commit -a -m "remove this module"
git push

However when I run new build I get and error from the plugin:

hudson.plugins.git.GitException: Command "/usr/bin/git submodule update --init --recursive --remote some-project" returned status code 1:
stdout: 
stderr: error: pathspec 'some-project' did not match any file(s) known to git.

I assume that git plugin should respect changes at superproject git repository , like removing some sub modules from there. But it seems it does not. Or I miss something. As far as taking a console git client it succeed on cases when sub modules gets removed:

git submodule init
git submodule sync
git submodule update --remote --init --merge --recursive