I decided to make the code that processes colour override information slightly smarter so that users can’t accidentally define an override without effect as that would use unnecessary memory.
I also had a thought about the options to remove unreferenced objects and panels as I found it particularly dangerous for LN3. A few elements (e.g. the flame of torches or the flag) are animated while the game runs and the animation uses objects from the Integrator file (rather than sprites), which are not cross-referenced in the file itself. So basically if you change anything in the list of objects or remove the unreferenced ones, all of a sudden the animations will misbehave.
I might have to withdraw the option. We shall see.