Start with ice.
Add heat.
Ice becomes liquid water.
Continue adding heat.
Liquid water becomes steam.
In these two reactions, the substance is transformed (from Ice, to Water, to Steam) but in every way retains the same mass and basic chemical composition - H2O.
Now, if you want a reason to have a Brilliant Energy Cold Iron Longsword, you can argue that the brilliant energy enhancement transforms the signifigant part of the weapon to light in a similar way that heat transforms ice to water to steam. The mass and the chemical composition remain the same. This case being argued, I would say that because of the retained chemical composition, the weapon still has the same effects.
"Can't make something out of [material] that doesn't have metal as its signifigant portion."
The Brilliant Energy Cold Iron Longsword is made of metal. It is beyond liquid metal, or even beyond vaporous metal -- it is light-metal. It is still metal, but only in a different state.
Of course, this is just an argument you could use. But if you want +4 enhancements to lose their weapon's material's DR bypassing, then by all means, say no. But it isn't an unreasonable argument.