Changing item color, inventory image

[Your Computer]

The issues you're coming across tell me you're running into original file conflict and possibly .map_cache conflict. When the game stores two files with the same name for later referencing, when searching for the file in its internal list it's going to pick the one it comes across first, which is the one stored in the Amnesia entities folder (even though the map stores the relative file paths anyway), because custom story files are always secondary and the game relies on the resources.cfg file. Also, if you have your environment set to create .map_cache files and the game did create one for the map you're testing, then that explains missing entities. The hpl.log normally has something to say about these things.