EF6 creating automatic migrations undoing explicit migrations

Question

I have a project that I've been developing for two years and has lots of migrations. However, I've recently had an issue with automatic migrations being created which undo my explicit migrations, meaning I can no longer build the DB properly. It happens on multiple (but by no means all) migrations and below is an example (from using -script) with a condensed and verbose version with names changed for easy reading:

Condensed version:

--first migration (201608150953102_Table1Migration)
ALTER TABLE [dbo].[Table1] ADD [CancelledReason] [int]
--explicit migration recorded in __MigrationHistory

--automatic migration added (201608151201077_Table2Migration_AutomaticMigration)
ALTER TABLE [dbo].[Table1] DROP COLUMN [CancelledReason]
--automatic migration recorded in __MigrationHistory

--second migration (201608151201078_Table2Migration)
ALTER TABLE [dbo].[Table2] DROP COLUMN [ManagerId]
--explicit migration recorded in __MigrationHistory

--automatic migration added (201609091123044_Table3Migration_AutomaticMigration)
ALTER TABLE [dbo].[Table1] ADD [CancelledReason] [int]
--automatic migration recorded in __MigrationHistory

--third migration (201609091123045_Table3Migration)
ALTER TABLE [dbo].[Table3] ADD [Active] [bit] NOT NULL DEFAULT 1
--explicit migration recorded in __MigrationHistory

Verbose version:

ALTER TABLE [dbo].[Table1] ADD [CancelledReason] [int]
INSERT [dbo].[__MigrationHistory]([MigrationId], [ContextKey], [Model], [ProductVersion])
VALUES (N'201608150953102_Table1Migration', N'Project.Migrations.Configuration',  0x1F8[...] , N'6.1.3-40302')

DECLARE @var0 nvarchar(128)
SELECT @var0 = name
FROM sys.default_constraints
WHERE parent_object_id = object_id(N'dbo.Table1')
AND col_name(parent_object_id, parent_column_id) = 'CancelledReason';
IF @var0 IS NOT NULL
    EXECUTE('ALTER TABLE [dbo].[Table1] DROP CONSTRAINT [' + @var0 + ']')
ALTER TABLE [dbo].[Table1] DROP COLUMN [CancelledReason]
INSERT [dbo].[__MigrationHistory]([MigrationId], [ContextKey], [Model], [ProductVersion])
VALUES (N'201608151201077_Table2Migration_AutomaticMigration', N'Project.Migrations.Configuration',  0x1F8[...] , N'6.1.3-40302')

IF object_id(N'[dbo].[FK_dbo.Table2_dbo.AspNetUsers_ManagerId]', N'F') IS NOT NULL
    ALTER TABLE [dbo].[Table2] DROP CONSTRAINT [FK_dbo.Table2_dbo.AspNetUsers_ManagerId]
IF EXISTS (SELECT name FROM sys.indexes WHERE name = N'IX_ManagerId' AND object_id = object_id(N'[dbo].[Table2]', N'U'))
    DROP INDEX [IX_ManagerId] ON [dbo].[Table2]
ALTER TABLE [dbo].[Table2] ADD [Manager] [nvarchar](max)
DECLARE @var1 nvarchar(128)
SELECT @var1 = name
FROM sys.default_constraints
WHERE parent_object_id = object_id(N'dbo.Table2')
AND col_name(parent_object_id, parent_column_id) = 'ManagerId';
IF @var1 IS NOT NULL
    EXECUTE('ALTER TABLE [dbo].[Table2] DROP CONSTRAINT [' + @var1 + ']')
ALTER TABLE [dbo].[Table2] DROP COLUMN [ManagerId]
INSERT [dbo].[__MigrationHistory]([MigrationId], [ContextKey], [Model], [ProductVersion])
VALUES (N'201608151201078_Table2Migration', N'Project.Migrations.Configuration',  0x1F8[...] , N'6.1.3-40302')

ALTER TABLE [dbo].[Table1] ADD [CancelledReason] [int]
INSERT [dbo].[__MigrationHistory]([MigrationId], [ContextKey], [Model], [ProductVersion])
VALUES (N'201609091123044_Table3Migration_AutomaticMigration', N'Project.Migrations.Configuration',  0x1F8[...] , N'6.1.3-40302')

ALTER TABLE [dbo].[Table3] ADD [Active] [bit] NOT NULL DEFAULT 1
INSERT [dbo].[__MigrationHistory]([MigrationId], [ContextKey], [Model], [ProductVersion])
VALUES (N'201609091123045_Table3Migration', N'Project.Migrations.Configuration',  0x1F8[...] , N'6.1.3-40302')

You can see that I'm focused on three concurrent migrations (these are about 20-30 migrations in), as they show the issue in a simple manner. The first migration adds a column, as expected, before the next migration triggers an automatic migration first, which wipes out the first migration's change. Then the third migration causes yet another automatic migration, which adds the column back in.

I don't understand why that is happening, so I'm hoping someone can shed some light on it.

Other possible pertinent information:

• Since I've been struggling with migrations I've reset the database back to the beginning using Update-Database –TargetMigration: $InitialDatabase so there's nothing that should be corrupting the migrations
• The first two migrations were created in different branches and later merged
• I'm the only developer on this project
• As well as the issue highlighted above, I also have automatic migrations being created to create tables that have already been created by explicit migrations, so getting errors telling me it's already an object. If I -script the whole update then I also see some tables being created and dropped multiple times in some instances, and some of those tables are still missing once the update has completed.