This seems like there’s something easy that I’m missing.
So, the problem: I’m having a problem debugging to the cRIO from WindRiver. If I debug a project on the cRIO, fix something, recompile, and then hit debug again, I get this dialog box. What is the proper way to debug something, then debug again without rebooting the cRIO?
Are you undeploying code and rebooting first so you don’t have anything already running on bootup on the cRIO?
The current WPILib will error out even if you solved the current problem. If the ~25 seconds for the cRIO to reboot (you can even do it remotely from WindRiver or the DS software) is a factor in your debugging process, I would seriously suggest you need to slow down and make your changes more methodically.
Or use python, which allows for a better and more responsive design cycle 
Previously I have been able to stop the RobotTask, unload my debug-deployed ‘.out’ file, and then could reload it from the debugger and start it again. This year, I have not been able to; I get strange exceptions. It seems that the only reliable way to deploy a new version for debugging is to Reset the cRio.