How to make sure change_tracking statistics stays updated

Since you are on SQL Server 2016 with DB compat mode, the behavior of TF 2371 is the default behavior.

You no longer have to enable trace flag 2371 in SQL Server 2016 or later because the corresponding behavior is enabled by default.

You should enable auto update async database option so that when sql server updates the stats, it does not affect your workload. Changing this db option is an online operation.

What you can do is to leverage sys.dm_db_stats_properties - new DMV to decide if you must manually update statistics for a table. You can have a sql agent job configured to check and update stats every x min or hour for certain key tables.

You might look into this. Kendra did a good write up on change tracking performance, and it's helped us as well.