I believe the repro is this:

• Create a template with an input variable
• Create a workspace and set the input variable to "foo"
• Update the template (but not the workspace) to delete the input variable
• Wait for auto-shutdown to happen

I believe you'll get an error that looks like the following:

A variable named "<X>" was assigned on the command line, but the root module does not declare a variable of that name. To use this value, add a "variable" block to the configuration.```

This ends up failing the terraform plan for the shutdown, and thus the workspace is not offline.