Judging by the error, could you have a look at the following path and check if there's a merged.lsf file in the folder?
\Data\Mods\YourMod\Levels\YourMod_Level\LevelTemplates
If there is, can you copy it someplace else as backup, then remove it?
Edit: Alternatively have a look into the level template folder (should be a separate level on its own), and see if you see any oddities within the /Instances/ folder there?
Here's a screen cap of how mine looks.