IF NOT EXISTS(SELECT * FROM [__EFMigrationsHistory] WHERE [MigrationId] = N'20201009100044_InitialCreate')
BEGIN
IF EXISTS (SELECT * FROM [sys].[identity_columns] WHERE [name] IN (N'Id', N'OrganisationId') AND [object_id] = OBJECT_ID(N'[Config]'))
SET IDENTITY_INSERT [Config] ON;
INSERT INTO [Config] ([Id], [OrganisationId])
VALUES (1, 1);
IF EXISTS (SELECT * FROM [sys].[identity_columns] WHERE [name] IN (N'Id', N'OrganisationId') AND [object_id] = OBJECT_ID(N'[Config]'))
SET IDENTITY_INSERT [Config] OFF;
END;

IF NOT EXISTS(SELECT * FROM [__EFMigrationsHistory] WHERE [MigrationId] = N'20201119082239_ChangedConfig')
BEGIN
DECLARE @var0 sysname;
SELECT @var0 = [d].[name]
FROM [sys].[default_constraints] [d]
INNER JOIN [sys].[columns] [c] ON [d].[parent_column_id] = [c].[column_id] AND [d].[parent_object_id] = [c].[object_id]
WHERE ([d].[parent_object_id] = OBJECT_ID(N'[Config]') AND [c].[name] = N'OrganisationId');
IF @var0 IS NOT NULL EXEC(N'ALTER TABLE [Config] DROP CONSTRAINT [' + @var0 + '];');
ALTER TABLE [Config] DROP COLUMN [OrganisationId];
END;

So, the initial create had a table Config with OrganisationId as a field. In a later build, it was dropped.
The migration worked fine at that point. Now, I have made more changes to the table, and the migration script fails with an error "Invalid column name".

Any idea why this is happening? The __EFMigrationsHistory does have the migrationIds, so looks like the script is getting evaluated before execution.

Any solution for this? Or am I missing something really simple?

Thanks for the help.