Nothing would go missing if the 2da are merged right.
Creature appearances would just have to move. Likely it would be easier to move Q resources into CEP 2da's, because I think Q has less to change over than CEP does. Blueprints would have to be manually edited I imagine to account for the change in position of the 2da.
Body parts like armor and such would have to be renamed to fit in places that CEP hasn't used, though I'm not sure how many empty places CEP has left in bodyparts 2da's.
Things that override in Q would just override normally if both hak sets were used together. As far as I know CEP doesn't override standard resources like Q does.
Weapon appearances would have to be renamed, though I think the Reforged from Q would just go together fine with CEP. Not sure. I don't think Q has a great deal in their weapons that CEP doesn't have. Might be best just to nix Q's weapons altogether.
Icons would have to be renamed to fit where CEP doesn't have content.
Shields, Amulets, and Rings, and I think Boots (?) would be the big issue. You'd probably have to just choose which flavor you liked. CEP or Q. You could probably go with Q's 3 part setup and just rename the appropriate models/icons to fit in the bottom slots... though it will probably be a bit more complicated than JUST that. Or you could just snatch the appearances from Q and add them into CEP without going 3 part.
Then there is the TLK merge, which is probably the most tedious part. They may share lines, I dunno. If they do then things get VERY complicated for scripts and editing many many 2da's to account for it.
You could probably just make a top hak that contained all these resources to put over CEP's to merge them. Q did a VERY good job keeping their haks organized. Chances are anything you need to rename to be compatible with CEP is all in one or two separate haks. Could just remove those from the list of used ones.
It can be done, just not easily. More time consuming than difficult. It would be better than trying to completely merge them in say CEP 2.7 or something. Some people don't want overriding content. Others don't want the tilesets Q has. Some people who use Q's content (myself) don't want CEP in their haks. A separate merge project just seems to me a better option as a 'Package' deal, rather than taking Q and forcing CEP users to have it. That way module builders/server admins can pick and choose a whole lot easier.