Don't worry about "doing something wrong". Just use tes4edit or wrye bash to undelete and disable the references. Somehow CK didn't delete those few rocks/trees you deleted properly. They contained more data than they should've, so that's a potential CTD in-game. Undeleting is essentially copying the reference (placed object in the gameworld or a cell) and setting its flag as disabled, plus changing its Z coordinate to -30000, so it would be well out of rendering range. Why is it importaint? Well, the game doesn't like deleted records. Say, if you delete a tree with your mod, and I make a mod that moves that tree, the game would most likely crash. Especially if there are persistaint (quest object) stuff involved. They tend to be permanently saved with savegame (just the coordinates and rotation), and the only way to get the mod working would be clean-save. Not really practical, nor popular method, if you have level 30 character. I'm not sure about skyrim, but with oblivion, if you need to move the door or whatever persistant object, you would actually need to DISABLE it and place a new one in a new spot. My advice to you is to keep on modding as usual, but use wrye bash or tes5edit to clean up the mod. Wrye makes it simple enough, altho tes5edit shows you exactly what your mod is changing with the game, and how it relates to other mods.