My rooted cutting has been growing really well, putting on about 3 feet of growth so far this summer and the trunk is noticeably thicker than when I first rooted.  However, when watering it yesterday morning, I noticed a hunk was sliced off the trunk about 3 inches above the soil line.  The slice is about a half inch wide and goes up maybe 2 or 3 inches.  I'm not sure what could have done it (we have quite a few rabbits and squirrels) but some of the missing piece was still attached at the top.  I've tried to fit it back where it belongs and then wrapped the area with parafilm to secure and protect it but I'm not sure if will make it.  This is my first tree so I was extremely disappointed to see it.  I guess next time I will have to make sure to root more cuttings so the loss of one isn't as big of a deal.  Is there hope for the tree and is there anything I should do to promote healing of the wound?

as long as there is bark connected on some part on the trunk then water should still be able to make its way up the tree. Also cover that part with soil my also encourage roots to grow. I don't know but that just my opinion and maybe what I'll do.   

You can add soil to a point above the gash, and encourage it to root above the gash.

Thanks for all of the quick replies!  AFB and pitangadiego, I hadn't thought about getting it to root like that, thanks for the suggestion.  Should I be concerned about disease if I am piling up soil where the gash is?  I have it covered in parafilm now (to protect it as well as hold the loose chunk in place, hoping it will heal).  Should I remove that before covering in soil?

Dan, thanks for the staking suggestion.  I have a stake in the pot already because it was starting to grow crooked when I repotted last (after being knocked around by a thunderstorm, as you stated).

I concur with Jon.
I saved many newly rooted cuttings by just up-ing the soil,
or transplanting them deeper.