Separate license file are needed if you want network licenses work in some unique cases even though you usually can combine different license files from the same vendor.
You have to fill out a Request Previous Versions in Subscription Administration under Manage License Benefits Use. Basically you request a new serial number for the survey 2006 companion from the CIV3D 2009 group.
Here is a user case (credit to Mike Caldwell) when this was needed and solved the issue.
We upgraded our license files to 2009 for CIV3D and AutoCAD but we are going to use 2006 products for a little longer until we test 2009. So now we are using LDD 2006 and we have a few of or survey guys needing to use the survey companion which in 2006 needed it's own license file. The autodesk people say it shouldn't need it's own file and will use 2009 to gets it's license. My question is do you know what serial number I should insert into the survey network deployment in order for it to see the license?
The following is an excerpt from autodesk.
As you may or may not know, Land Desktop Companion will pull a Civil 3D license if no Land Desktop license is available. However, for the 2009 products, there is no such thing as Survey. The functionality that was in Survey has been wrapped into Land Desktop Companion. That being said, you will still need to have your Survey 2006 license increment in your license file to run Survey 2006.