As long as you're using a compatible rom I think it should be fine. Nandroid beforehand though!
If your ROM is based on one of the kerneltypes which can be selected in the kitchen then I think it should be fine, also the kitchen will tell you if it failed to cook your zip file!
If your ROM is based on one of the kerneltypes which can be selected in the kitchen then I think it should be fine, also the kitchen will tell you if it failed to cook your zip file!