If you have assembled documents you can still upgrade contract workspaces for amendments - although it makes supporting the changes more work. This is the process we use.
1) Create a new version of the contract template and make any required modifications (do not publish yet)
2) Make a copy of the template
3) Rename the original template to something like "<original name> - variations only" and put it in a new folder where you will store templates that are only being kept around for variations to existing contracts.
4) Delete all assembled documents from the template. Since no new contracts will be created this is OK. Contracts that are being amended already have a contract document.
5) Make the origiinal template only available on a condition "Is_Amendment" which is true only when an amendment is being made. This stops new contracts being created with it but allows existing contracts to be amended.
6) Publish the original template
7) Rename the new template to <original name> and publish it. This is now the template for new contracts.
You will need to follow this process any time you make any changes.