How can I fix a migration input format mess?
One option is in the migration template, to add the input format value.

I found the default_value plugin worked well there e.g, to set default full_html:

field_subheading:
  plugin: sub_process
  source: field_subheading
  process:
    value: value
    format:
      plugin: default_value
      default_value: full_html


Another option, could be to run an SQL query to update the field data and revision data tables

update node__field_subheading set field_subheading_format = 'full_html' where field_subheading_format = 'other_format';
update node_revision__field_subheading set field_subheading_format = 'full_html' where field_subheading_format = 'other_format';


then clear cache.

However fixing as part of the migration template mapping is recommended.