I've merged a few default replacement textures without issue, such as roads, skins and other minor replacements. What is it you were trying to merge but couldnt? Dont forget to clear your caches. I also didnt bother merging hacks/tweaks/careers etc, as I'm always wanting to adjust them or update them.
Actually...taking another look, remerging my default replacements, clearing my caches and reloading my game they are now loading in .dbc files. I think I may have had some conflicts as I removed some files when I remerged.