It's possible and even probable that the save you loaded up with Kopernicus isn't easily recoverable but the rest should be salvageable. We'll need your logs to even begin to guess at what has broken them though.
Edit: Actually I'll just take a swing since it's likely: if the game crashed while saving, it's possible the persistent.sfs of the game you loaded when Kopernicus installed was corrupted and KSP is throwing an unhandled exception while trying to parse it. This will cause a chain reaction of failure: most likely, clicking "Resume game" will appear to do nothing at all while the log (Alt+F2) prints an exception
Try moving or deleting that save's folder