IIt's important to unmount the Easy Debian image before replacing it. Otherwise there will be inconsistencies (e.g. remaining menu icons). The easiest way unmount it is to click the "Close Easy Debian" icon. Then it should work fine.

As for copying images: You might have noticed that copying data takes way longer than moving it (especially on a relatively slow computer like the N900), because moving doesn't actually move data but is only a rename as long as the partition stays the same.
Therefore it would be wise to have all your images on the same partition. Exchanging them then is a bit like playing the towers of Hanoi.

Just befaore I bought my N900 I tinkered with getting a Debian chroot to work in a rooted Android 2.2 SDK but I wasn't successful because 2.2 didn't yet support ext4 (or any other ext file system) and I was not able to add that support.
However some 2.2 custom builds made by people with more skills than I have included ext4 support and 2.3 even came with it as the system's file system. ext2 is also supported. So on a rooted 2.3 or a custom 2.2 a chroot should be no problem. You'll find reports for working chroots on Motorola Milestones (I don't remember the version). I don't know about GUI or sound support.