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We used to have Parent departments Inactive (as to hide them off lists) but kept the Children as active. However, we've had to add some new child departments to the inactive parents and when re-inactivating the parents it also sets the children as in-active. Any idea what gives

I normally just export a csv list of all department, with internal id, inactive, name, column.. I will use this to update the department list back to its current state after I activate them all and added the children

Tried this previously. I might try again and disable the run suitescript setting

inactivate them from the list of departments using the checkbox

Don't inactivate them from the record itself - it will inactivate the children with it