If the name of the primary key has been changed on the local database, then SQL Compare will issue a 'drop constraint' to recreate it using the new name, but that doesn't seem to be allowed in Azure:
The following error message was returned from the SQL Server:
 Tables without a clustered index are not supported in this version of SQL Server. Please create a clustered index and try again.
Could not drop constraint. See previous errors.
The following SQL command caused the error:
ALTER TABLE [files].[DataAvailability] DROP CONSTRAINT [PK_DataNotAvailable]
As a minimum, you could include a warning in the warnings list, alternatively do a full table rebuild instead, as you do with major datatype changes (when you see that the target is Azure).
Another idea would be to include a sort of "Quick-options" for Azure targets, so that the user easily could set all the necessary Ignores to make it work.
Thanks for a wonderful product.