Django deleted migrations directory

You could just reset your migrations to before your initial migrate and start over. This doesn't delete data in the database, but rather resets the tracking of your migrations. If all of your databases are already migrated to the same level, then you can start over in your migration tracking.

There is a StackOverflow question here that already addresses it:

How to reset migrations in Django 1.7?

In short,

./manage.py migrate --fake <app-name> zero

This resets the tracking to prior to your initial migration.

And then,

./manage.py makemigrations <app-name>
./manage.py migrate <app-name>

Which recreates the initial migration and applies it.

As always, if your data is important, make a backup first.