To be on the safe side, prismic.io will keep any existing data after a custom type has been modified. We separate the editing app from the API, so if you make changes to the custom type without publishing anything, your API will not change.
This means, for instance, if you delete a field in a custom type, this will only make that field disappear from the writing-room editor. For any document that existed before the field was removed, that field and its contents will still be saved with that document.
This gives a huge flexibility to the way you model your content.
Behavior with API v1
If you remove a field from your custom type, the API v1 will always display this field and its content.
You will be able to see this data in your editor by re-adding the field to your custom type using the same API-ID as it originally had.
Behavior with API v2
If you remove a field from your custom type, the API v2 will not display this field.
The data will still be saved, it just won't appear in the API response. You will be able to see the data again if you re-add the field to your custom type using the same API-ID as it originally had.