Running database updates causes issues on amp.settings.yml

When running database updates

$ drush updb -y
and then run
$ drush cim -y
you get an error

`[Exception]`
`The import failed due to the following reasons:`
`Deleted and replaced configuration "amp.settings"`

and this is because on hook update functions it tries to write data when NO yet the configration file has been created as a consequence throws above error.