Remove all previous versions of certain files in a repository. Only keep the latest

I have a repo with many binary files that had several versions commited and pushed. I want to keep only the latest version of all those files.

It's ok to force a push. I'm the only one working on this project.

I have local changes I don't want to lose too. They aren't commited yet.

Your task it is not so trivial, but I would suggest you to use BFG Repo-Cleaner.

As you can see reading the documentation, it can do many operation on repositories, for example remove files matching any criteria you want, but the most important thing is the following:

> Your current files are sacred...
>
> By default the BFG doesn't modify the
> contents of your latest commit on your master (or 'HEAD') branch, even
> though it will clean all the commits before it.
>
> That's because your latest commit is likely to be the one that you
> deploy to production, and a simple deletion of a private credential or
> a big file is quite likely to result in broken code that no longer has
> the hard-coded data it expects - you need to fix that, the BFG can't
> do it for you. Once you've committed your changes- and your latest
> commit is clean with none of the undesired data in it - you can run
> the BFG to perform it's simple deletion operations over all your
> historical commits.

Thanks to it you could remove blob matching some conditions, but keeping the latest version.

Further, keep in mind that BFG creates a second repo locally, so it does not change anything in your main repo. If all goes as you expect you can push forced to the remote server.