I have done this for a customer on a large scale and it worked absolutely fine.
I would go to the blpackage, export it. The only difference was I was excluding the blpackage, which does not matter here. While importing the same directory structure was taken. I think the structure is taken from the bldeploy.xml in the export file. If you can give me your email address, I will forward you a document which I had made as How The export/import of blpackages and depot objects would work. Ideally, if you export correctly, it should import with the same directory structure.
is the BL Appserver and console version same in both the environments?