Non-trivial git rebases fail and cause Qt Creator to freeze

With a CMake project when I try to do a git rebase with non-trivial changes like moving renaming files (including sub CMakeLists.txt files) while Qt Creator has the project open then the rebase fails:

$ git rebase -i origin/master
... | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
error: cannot stat 'xxx/xxx': Permission denied
error: cannot stat 'xxx/xxx': Permission denied

And Qt Creator becomes unresponsive and must be force killed.