I had the same problem. I used this manual migration, and so far I have not encountered any additional problems.
public override void Up() { RenameColumn(table: "dbo.AspNetUserClaims", name: "User_Id", newName: "UserId"); RenameIndex(table: "dbo.AspNetUserClaims", name: "IX_User_Id", newName: "IX_UserId"); DropPrimaryKey("dbo.AspNetUserLogins"); AddColumn("dbo.AspNetUsers", "Email", c => c.String(maxLength: 256)); AddColumn("dbo.AspNetUsers", "EmailConfirmed", c => c.Boolean(nullable: false)); AddColumn("dbo.AspNetUsers", "PhoneNumber", c => c.String()); AddColumn("dbo.AspNetUsers", "PhoneNumberConfirmed", c => c.Boolean(nullable: false)); AddColumn("dbo.AspNetUsers", "TwoFactorEnabled", c => c.Boolean(nullable: false)); AddColumn("dbo.AspNetUsers", "LockoutEndDateUtc", c => c.DateTime()); AddColumn("dbo.AspNetUsers", "LockoutEnabled", c => c.Boolean(nullable: false)); AddColumn("dbo.AspNetUsers", "AccessFailedCount", c => c.Int(nullable: false)); AlterColumn("dbo.AspNetUsers", "UserName", c => c.String(nullable: false, maxLength: 256)); AlterColumn("dbo.AspNetUsers", "FirstName", c => c.String(nullable: false)); AlterColumn("dbo.AspNetUsers", "LastName", c => c.String(nullable: false)); AddColumn("dbo.AspNetUsers", "CreatedDateTime", c => c.DateTime(nullable: false)); AlterColumn("dbo.AspNetRoles", "Name", c => c.String(nullable: false, maxLength: 256)); AddPrimaryKey("dbo.AspNetUserLogins", new[] { "LoginProvider", "ProviderKey", "UserId" }); CreateIndex("dbo.AspNetUsers", "UserName", unique: true, name: "UserNameIndex"); CreateIndex("dbo.AspNetRoles", "Name", unique: true, name: "RoleNameIndex"); DropColumn("dbo.AspNetUsers", "Discriminator"); }
Taken from: http://adamstephensen.com/2014/05/02/upgrading-from-asp-net-identity-1-0-to-2-0/