I'm just posting this in case other people are having similar problems with their Nook Color's running CyanogenMod 7 off SD cards. While I've been mostly satisfied, I have also been frustrated by some frequent (5-10 a day) force close messages (usually gapps or google framework related), some apps that just seem to always throw force close messages (a comic reader), and some files which suddenly become unreadable by the apps that generated them. I had assumed the problems were just teething related to the rapid pace of development in getting Android Gingerbread on the Nook Color, but so few other people seemed to report the problem. So today after losing a two documents I'd written on my device I had enough; the files were still on the device, had the right permissions, the right ownership, and I could view the contents as text, but the app which created them refused to open them. I decided to try the eMMC route and ditch the SD cards in favor of a phiremod install of CM 7. Remarkably in the day I've now been using this eMMC install I haven't had a single force close, if I was still running my old set up I would have had at least 5 by now. It appears installing the OS to internal memory has resolved all my problems.
To try phiremod yourself, read my phiremod instructions install and configuration guide.