I heard my name, so here I am! Washington and iggey are correct. TES4Edit contains a feature (pretty much requested by Arthmoor and myself) which will automatically undelete every deleted object in a mod (whether originally from Oblivion.esm, or from some other master file), set it's Z coordinate to -30,000 and mark it disabled. Marking it disabled is all you actually need to stop the game loading it into memory and affecting FPS, but of course it's still visible in the CS, and makes modding difficult. To resolve this, I suggested to Elminster (creator of TES4Edit) that the object be dropped out of sight, and after some experimenting, I discovered that -30,000 is the lowest value the CS will allow before throwing up a warning message (at -30,001 or lower, you'll get a warning for each object, suggesting that it's misplaced. Harmless to the mod, but annoying to the modder).
J.O.D. is correct, if one mod deletes an object from a master file, and another mod loading afterwards edits that same object, the game will crash on exit, guaranteed. But if the object is instead disabled, then there are no problems.