How to fix EF code first approach on exisitng database.

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C#

ASP.NET

Visual-Studio

C#4.0

MVC

, +

Hi,
I have a created two separate C# web application using EF6 (one with Database First and other with Code First approach). everything is going on smoothly but after sometime it is required to merge both.
After merging , Database is same for Code First Approach.
Initial I was using 'MigrateDatabasetoLatestVersion' for database initializer.
So when I try to run my application , it throws error related to Table is already exist. I have also tried with Package manager console to update migration and it throws same error.
and so I was not able to run the new solution on same database.

For resolving this issue, I have changed database initializer to 'CreateDatabaseifNotExist'. and after that I am able to use this database with my new solutions.

But the Problem arise, when I tried to add a new column to existing table or Creating a new table with Code First approach. Since there is no migration so it skips to alter/add table and for that I have to manually run Alter/Add table Script with each changes.

Is there any valid solution for this?
either MigrateDatabasetoLatestVersion doesn't throw exception or it is not required to run db script each time.

Thanks.