I have a workflow that that works very well but I now need to make a change to it.

I have had no issues with minor changes to Workflows (email address changes).

However on my next change I need to modify some paths and create new folders and new approval process. 

When I publish this, does this break the workflow on existing documents that are currently still in the system, waiting for their next steps?

As long as the new documents go to the new locations, and the existing documents carry on with the old version I am happy.  As both versions end up in the same ending folder, but now have a different approval path.