Git merge directories that have become separated

Git merge directories that have become separated

Not quite sure how to explain this clearly, but here goes.
Due to a bug in Tortoise-git, we've ended with a situation like this;
All our code should be under a directory structure like this (this is
Symfony2 project);
src/XYZ/OurExitingBundle
src/XYZ/AnotherExcitingBundle
but, due (we think) to the bug in Tortoise-git, when we pull the code onto
a linux box, we've got;
src/XYZ/OurExcitingBundle
src/XYZ/AnotherExcitingBundle
src/xyz/ourexcitingbundle
src/xyz/anotherexcitingbundle
(i.e. the actual directories, plus a lowercase equivalent). The files
making our project seem to be split randomly between the CamelCase and the
lowercase directories.
As we are developing on Windows machines, this does not matter whilst
coding, but when the code is pushed to our linux server, everything falls
over, as files are not where they are supposed to be, or a file exists in
the CamelCase directory, but a newer version is in the lowercase
directory.
So, my question is, is there a way to "merge" all the files in the
lowercase directories into their equivalents in the CamelCase directories,
ending up with all the latest code in just the CamelCase directories?
Many thanks in advance for all help.