First you need to shut down any app that is using the datastore. The app holds the file in memory while running and flushes it to disk when it shuts down. This means any writes you do while the app is running will be undone when you shut down the app.
Next, find the datastore file and connect to it using sqlite.
user@host:path$ sqlite3 my-app.sqlite3
Check out which tables exist. You will see your app's data stored in a table that is prefixed with dev~<project_id>
.
sqlite> .tables
Apps
IdSeq
Namespaces
ScatteredIdCounters
dev~<project_id>!!Entities
dev~<project_id>!!EntitiesByProperty
Get a list of which Kinds exist in your application
select distinct kind from "dev~<project_id>!!Entities";
Delete the Kinds you want removed!
delete from "dev~<project_id>!!Entities" where kind IN ('Kind1', 'Kind2', 'Kind3');