It seems there was a mix-up somewhere, as the edit-data gro file for the Jewel of the Nile includes a lot of resources from the main game. Now, you may know that resources from the DLC will not work for people without the DLC. Since these resources are marked as DLC content (even though they aren't), this means that, chances are, if you have the JoTN DLC and you've used resources from the main game for your mod, your mod will not work for people without the DLC.

The content this affects includes, but is not limited to:
-Enemy models
-Weapon models
-Enemy parameters and behaviours
-Item Parameters
-Weapon Parameters
-Destruction settings
-Materials
-Projectiles
-Netricsa Messages
-Character Tools

I've submitted a bug report on this to the tracker (Bug 28693), so hopefully things will get sorted out soon. For the time being, those of you who have the DLC and wish to avoid this, either rename your JoTN edit-data gro (currently "DLC_Sam3Extended_193968_edit.gro") so it has a different file extention (like, say, ".zip"), or move the said gro outside of the "SeriousSam3" folder. This will stop the gro from being loaded, and you can work with the files without fear of them being marked.

Now, even with this done, any saved content that was marked as DLC-only will still be marked as DLC-only. There is no easy fix for this; You'll have to revert back to the original files and re-do any changes you made to the affected files. Figuring out which files were mistakenly marked as DLC will be a pain, but I've submitted a suggestion for making that easier (Bug 28692).