The issue is the native HDFS protocol is different between, 0.20.2 (the couple of year old version) and CDH3. The newer versions of hadoop 0.20.20x have also changes in the protocol and they should match CDH3. You would run into the same issues if you were using different HDFS clusters with different versions of hadoop and wanted to copy data between them using distcp (NOTE: You can make it work by using the http version of the FS).
So to make a long story short if you use the same version of Hadoop CDH or Apache across different clusters everything should work fine.
Aaron