In my MVC application I used Entity Framework 6 and created database with code first approach. After a certain time, I updated one of the entity classes by adding new column
Why did you do steps 1-4? That's where you went wrong. If you had a previously generated database and you're just making changes to the schema, then just generate a migration and apply it. By doing steps 1-4, you're effectively undoing Entity Framework's knowledge of this database and essentially ending up with code-first with an existing database. At which point, you either have to manually change your schema or let Entity Framework blow it out and start over.
As far as getting back to a state where you can apply migrations again goes, you were on the right track with generating a migration and just emptying out the Up method. However, you need to do this against your application's previous state, i.e. the one that matches the database as it currently is. Otherwise, Entity Framework is going to generate create tables that include your code changes. So the steps to follow are:
Up methodupdate-databaseAfter that, you should be good to go again. Then, the next time you make code changes, just follow steps 5 & 6.