Good news, I found a solution. I first tried to migrate the missing records directly from the DancingGoatMvc database, but that didn't work, so I tried using Continuous Integration for this task.
These were the steps to restore the missing Transformations:
- Take a freshly installed Kentico DancingGoatMvc application
 
- Enabled Continuous Integration in the DancingGoatMvc project and do a full export
 
- Add the E-Commerce Transformation related files to the broken application's CI Repository folder
 
- Also update 
@global/cms.rolepermission/cmspowerusers because the permissions for the transformations were gone. 
- Run 
ContinuousIntegration.exe -r on the broken application. This will restore the missing records 
- After the import, resign all Macros in the System application
 
These are the records, that were missing:
@global/cms.classpermission/cms.documenttype_ecommerce.transformations/
@global/cms.classsite/ecommerce.transformations@fb7e4dff0d.xml
@global/cms.documenttype/ecommerce.transformations.xml
@global/cms.transformation/cms.documenttype_ecommerce.transformations/
Those are the files I had to modify. I also modified the updategeneral.xml files because the hash was different. However, I'm not sure if this was necessary and I don't know if other files need to be modified as well. Everything seems to work fine now.
@global/cms.rolepermission/cmspowerusers@2dbb5e9e4b.xml
@global/cms.alternativeform/cms.systemtable_ecommerce.order/updategeneral.xml
@global/cms.alternativeform/cms.systemtable_ecommerce.sku/updategeneral.xml
Thanks