In general, I wouldn’t recommend DeepFreeze for many reasons, but I do realize that isn’t a sufficient answer when you often don’t have a choice.
You can delete the duplicate records using a tool IBM provides: TEM Computer Remover
Looks like there is an old whitepaper: http://www.faronics.com/assets/DFEnt_BigFix.pdf
It would be best to prevent the creation of duplicate computer records in the first place by getting Deep Freeze to play nice with BigFix.