Aren't you eventually doomed to find yourself entering some distortion of spacetime during your deep space travels? Unless of course you're just thinking about keeping track of time relative to you and the Earth refugees.
I think we'd mostly be concerned with keeping track of time relative to the other earthlings, as I'm pretty sure we'd never have a reason to measure the lifespan of a bug living on the rim of a black hole.
If the Earth is gone, use the planet we are traveling to as the new way to measure days/years. That's simple enough, and the best solution.
Half of the earthlings decided to trip over to http://en.wikipedia.org/wiki/Sirius and they want Christmas cards too.
the yelling of the crew protesting nuclear power from a battery.
The protests will last till the end of the universe! We're saved!
The ship was fixed, but that won't get the time back.