Windows and Git issue with illegal filenames

So, I am working on a component of my company project in which we use git as our version control. After I finished my task on the project, I needed to submit the code for verification.

The problem is I am running on a windows machine with perl filenames on a remote git branch, something similar to "filename :: 123.pm" . So what Windows does when I checkout that branch is just remove them from my local branch and all the filenames with :: are gone. Since these are important files this is a problem for my additions in the local branch and cannot be merged since the important perl files are gone.

How can I avoid this?

I wanted to try something like ignore specific files for the git clone of the repo, so when I checkout they are ignored and not removed, but that is not possible. Another thing I wanted to do was clone in a VM running Linux and work from there to make commits. Well cloning is very slow and that's not an option either.

What is my best option for working with this repo where the filenames are not valid for the Windows machine to read? And no, renaming the files won't work as there is a lot more to do to do that if we do.