Thanks.
So the only thing we can think of is that the clone of the git repository in circleci has some references that are no longer valid.
Could you please add, to the P/R, the following to the runsonar.sh (in the method gitFetch, for example):
git fetch --all
git branch -D master
git rev-parse origin/master
This will update all remote references, delete local master branch (if exists) and print the current remote reference to master.