Thanks for that. I've got a few more questions to clarify what's happening:
1. Can I confirm that you are using SQL Compare to deploy your schema changes rather than SQL Data Compare to deloy static data changes?
They are two distinct products and SQL Compare will not try to compare data changes.
2. When you unlinked the static data tables, did you commit that change to SQL Source Control? As the unlink operation should appear in the commit tab.
3. Are you making a change to the schema for the static lookup table that has showed up when doing your initial comparison? If so, is it possible this change could cause data loss?