Whenever the bundle reports executed unavailable migrations it means that there are migration identifiers in the migrations_versions database table from when you previously ran it.

To get rid of the notification, make sure that when you delete a migration file, delete its corresponding identifier from the database table.

You can do this with (or manually):

php bin/console doctrine:migrations:version YYYYMMDDHHMMSS --delete

Or, rewind the migration with:

php bin/console doctrine:migrations:execute YYYYMMDDHHMMSS --down

but this will run the down function of that migration file undoing whatever it set and remove it from the database.

I have tried

php bin/console doctrine migrations:version YYYYMMDDHHMMSS --delete

and

php bin/console doctrine:migrations:execute YYYYMMDDHHMMSS --down

but it works only if we actually have migration.

I asked about situation when migration is deleted. But thanks DevDonkey for information about migration_versions table.

My solution is, to run

php bin/console doctrine:migrations:status --show-versions

and see

And delete from migration_versions these rows.

Once you deleted them, you can simply :

DELETE FROM doctrine_migration_versions;