Reversal of cross-linking in ChIP-seq
After the crosslink reversal step, you still have some DNA connected to protein fragments.

So at that step, instead of doing a normal DNA purification, we also need to use a phenol-chloroform extraction or special columns to seperate DNA from protein fragments. 

Thermofisher usually gives really good explanations too.

Please let me know if I didn't understand the question correctly! :)