Missing spec re-adjustment after spec divergence

Hello,

My scenario/problem is following:
1. create spec that is quite good, plan, tasks, all works well
2. Implement spec
3. Find out that there are things not specified, simplified, wrongly specced, or simply not working as intended
4. Do changes to make it good
 
 Then my problem is how to re-integrate all changes back to spec, plan, tasks so there is less noise on subsequent implementations?