I'm seeing the same issue, compounded by the fact that even clearing down the workspace doesn't resolve the problem. In the output below (censored for security/privacy reasons, intent is the same). origin/requirejs-2.0-upgrade is not part of REMOVEDPROJECT-pkg, but a branch in the submodule contained with in.
This did work, but after changing the submodule locations and updating via git submodule sync each build gets the following error.

Work around will be to add a git checkout as a manual step, so not entirely a blocker but a significant problem none the less.

Jenkins ver. 1.473

Jenkins GIT plugin      org.jenkinsci.plugins:git:1.1.21	
annotation-indexer      org.jvnet.hudson:annotation-indexer:1.2	
Joda time               joda-time:joda-time:1.5.1
JSch                    com.jcraft:jsch:0.1.44-1
Bridge method injection com.infradna.tool:bridge-method-annotation:1.4
annotations	
JGit - Core             org.eclipse.jgit:org.eclipse.jgit:0.12.1

Building remotely on RPM build slave 1 in workspace /home/jenkins/workspace/REMOVEDPROJECT-pkg
Checkout:REMOVEDPROJECT-pkg / /home/jenkins/workspace/REMOVEDPROJECT-pkg - hudson.remoting.Channel@aef8664:RPM build slave 1
Using strategy: Default
Last Built Revision: Revision e0fb13e7b464d812a90d7d73b1df06cf09d27c56 (origin/requirejs-2.0-upgrade)
Fetching changes from 1 remote Git repository
Fetching upstream changes from git@gitlab.REMOVED:REMOVEDPROJECT-pkg.git
Seen branch in repository origin/HEAD
Seen branch in repository origin/master
Commencing build of Revision e0fb13e7b464d812a90d7d73b1df06cf09d27c56 (origin/requirejs-2.0-upgrade)
Checking out Revision e0fb13e7b464d812a90d7d73b1df06cf09d27c56 (origin/requirejs-2.0-upgrade)
FATAL: Could not checkout null with start point e0fb13e7b464d812a90d7d73b1df06cf09d27c56
hudson.plugins.git.GitException: Could not checkout null with start point e0fb13e7b464d812a90d7d73b1df06cf09d27c56
	at hudson.plugins.git.GitAPI.checkoutBranch(GitAPI.java:931)
	at hudson.plugins.git.GitSCM$4.invoke(GitSCM.java:1285)
	at hudson.plugins.git.GitSCM$4.invoke(GitSCM.java:1269)
	at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2196)
	at hudson.remoting.UserRequest.perform(UserRequest.java:118)
	at hudson.remoting.UserRequest.perform(UserRequest.java:48)
	at hudson.remoting.Request$2.run(Request.java:326)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
	at java.util.concurrent.FutureTask.run(FutureTask.java:166)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
	at java.lang.Thread.run(Thread.java:679)
Caused by: hudson.plugins.git.GitException: Command "/usr/bin/git checkout -f e0fb13e7b464d812a90d7d73b1df06cf09d27c56" returned status code 128:
stdout: 
stderr: fatal: reference is not a tree: e0fb13e7b464d812a90d7d73b1df06cf09d27c56

	at hudson.plugins.git.GitAPI.launchCommandIn(GitAPI.java:838)
	at hudson.plugins.git.GitAPI.launchCommand(GitAPI.java:800)
	at hudson.plugins.git.GitAPI.launchCommand(GitAPI.java:810)
	at hudson.plugins.git.GitAPI.checkoutBranch(GitAPI.java:918)
	... 12 more
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