Anyone have a good way to export large number of documents and files from eB?

We need to export a large number of drawings and related files from eB to a repository so that they can be imported to another system.  But we keep getting errors with disk space whenever we try to export more than 100 at a time using "get all files" option from the basket and same with publisher.  

Wondering if there are any other options for performing this type of task that would be easier and more stable.  Not sure what is the reason behind this as we don't seem to have any problem with either of these processes for exporting more than 500 documents at a time in our test/training environments.