Well it depends, most of all, car mods and simply mods will be the hardest of it. Since some mods are GTAIV and EFLC Only, and only some are converted to both. But to your question, I highly think and somewhat know that some files may be replaced, such as your Directory, or some files such as ENB will be replaced. If the files aren't converted, such as for example if you have ENB for GTAIV only, and you move ENB to EFLC Folder, It's very likely for the ENB to not work or it will cause a sudden crash. And yes, the GTAIV directory will be saved in the folder and EFLC should be located next to it.