Regarding "rebuilding" - are you referring to: a specific city plan or individual plots? If it is individual plots, check your settlement build size in upper right corner of HUD, see image, and then use the Y (controller for me) at the Workbench to increase the size, see image.
In mid-game, I occasionally see a settlement's happiness drop (I micromanage). After investigating the cause it was frequently due to the settlement size limit. One or more plots are trying to upgrade, but due to the size limit, the upgrading stops and the associated resource is not counted in the total, e.g. food. So after some period of time, happiness drops due to insufficient food. Travelling to the settlement and increasing the build limit allows the plot upgrade to continue which fixed my problem. You will need some patience (not one of my strong suits
) to allow the scripts to "catch up."
Hopefully this will fix your situation.