ya sounds like you'll be just fine. Remember to let her recoop from all that shock. What i do is lollipop all the bottom sets off of my clones that have been vegging for a week and use those as new clones and dispose of the rest , followed by throwing them into flowering after they recoop. I have literally cloned off of a clone more than 3 dozen times now and counting. At some point or another i hacked up my plants pretty good and they still regained and fed more clones.
if you have a pic i can look at before you cut them back that would help alot . But again i hack off nearly 40% of my plants before they go into flower because of my space,light,etc etc. i just never recommend cutting the main stem unless she is really tall and is a must.