Try calling again and asking for Account Services. This is assuming the upgrade fees were charged by sprint, not radioshack.
You'll have to be a little silver tongued, and work a little bit of charm in there. Account services is the dept that has the authority to provide refunds and credits to your account with ease.
If you have a premier account, the primary phone is exempt from upgrade fees, this is part of being a premier customer. If you sense resistance from them, explain very nicely how you are loyal sprint customers..blah blah and work some magic.