I did a bit of digging and as I thought this behavior has changed from 2.0.x to 3.1.x
in 2.0.x the SQLFileChange.java checks for the existence of the file.
in 3.1.x this functionality has been moved to StreamUtil.java where no such checks are done.
I was going to submit a bug, but the git repository does not seem to be setup to allow it.
EDIT: issues are in jira. They have a bug for this - CORE-1828
cheers,
Florian