We switched pc's and we were able to reboot the cRIO in safe mode, and reformat it from there. We called National Instruments support number (check their website if you need it.) and they walked us through debugging. They wound up having us change a few things within cRIO FTP server. After that we were still having problems with getting the cRIO to respond. It turned out there was a problem with the digital sidecar because one of the ports went bad. We moved a PWM cable, then both sides of tank drive started to respond
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Thank you all for the help!