Adding And Removing Fields To CiviCRM Tables
I think the civi process works great for adding columns. Dropping columns is not done too often and hence the above error.

I suspect the easiest work-around might be to empty out the civicrm_generated file:

echo '' &gt; civicrm_generated.mysql


and then run regen.sh (this basically makes setup.sh load an empty file, and hence avoid the error). Maybe this should be part of the regen.sh script