Ok, so I spent a significant amount of time searching. Windows has a limit of about 250 characters for file names and paths. Android/Linux does not. Windows 7 has something called robocopy that can be run from the command prompt to address the issue of not being able to copy long file names. Filename/paths can be up to 32,000 characters or some nonsense like that with robocopy....
If you have encountered this problem, here is what I did:
-Create a shortcut on the desktop for "cmd".
-Right click and run as administrator (you will get an error if you don't do this)
-Put both SD cards into your computer and identify which one you are copying from and which one you are copying to. (alternatively you can go from card to PC and PC to card but it takes twice as long)
-robocopy /e /copyall SourceDrive:\ DestinationDrive:\
In my case, source was F:\ and Destination was G:\ as those were the locations of my SD cards.
I'm not certain that /copyall was necessary. That may be the default. Without /E, it did not copy subdirectories the first time...
Hopefully this saves someone a headache in the future.