Amit Banerjee mentions a new stored procedure for change tracking cleanup:
In SQL Server 2014 Service Pack 2 and above, we provided a new Stored Procedure, sp_flush_CT_internal_table_on_demand, to assist with Change Tracking cleanup. KB3173157 has more details. This stored procedure accepts a table name as parameter and will attempt to cleanup records from the corresponding change tracking internal table. During the course of the deletion, it will print some verbose in the output window about the progress of deletion.
If automated change tracking cleanup works well enough for you, there’s no change; but if you’re struggling with that cleanup, this procedure might help.