The simplest solution is to clone that third-party repo, reproduces your fix, commit and push (if you have access to their repo, you if you have forked it on GitHub)
If not, do (in a fresh clone of your repo) a:
git ls-tree HEAD Src/Foo/FooBar
See if there is an special entry 160000
, which would indicate that FooBar was registered as a submodule at one point in time) even if the .gitmodules doesn't list FooBar anymore.
A git rm --cached Src/Foo/FooBar
(with git 1.8.5+) would take care of that submodule entry.
Of course, if the thirdparty sources are not part of a git repo, then adding them in a different folder within your own repo would work too.
But the history of those third-party library files would become mixed with the history of your main repo.