Oh yeah. That can lead to unbelievably frustrating problems, like backups not restoring and system not mounting and worse. Get rid of the old one and go with the current stable through ROM manager or through the flashable zip in the development thread. ClockworkMod version 126.96.36.199. The last thing, seriously, I think, with the Nook (which is basically unbrickable), the last thing you want is incompatible CWM. The nook itself would still be safe, but all your data and apps would be in serious jeopardy. They would be salvageable, but it would take a detailed and grueling work around.
Get rid of the old, and in with the new. You would still have the folder on the SDcard, but now it will actually have some value.
Edit: If you already have backups you want to keep made in an outdated CWM, let me know. There is a work around, but it involves multiple flashing.