We are using a 7D and Zoom recorder. Is there a reason we should be keeping the original folder structure, created by the devices for the cards, to store our raw material? The Zoom recorder in particular creates many seemingly unnecessary folders and it would be nice to clean it up.
I know that in Final Cut Pro when using a certain EOS plugin with Log & Capture the plugin would only recognize folders built the same way as the SD card. I'm not sure if something like that will arise in Avid, especially when trying to link our transcoded material back to the original H.264 footage.
ALWAYS keep the folder structure. FCP needs it, Avid does too if you want to use AMA. You never know what the future will hold in terms of what NLE is around, and how it will deal with tapeless footage, so it is always wise to use the original folder structure.
With cameras. I don't think the same applies for audio...but I am not sure. I always play it safe and keep everything the way the devices recorded them.