Hi,
The standard process of upgrading backup the /etc/crowdsec content, deletes it, and recreates it. Then it restores the content existing before the upgrade, so it should not affect this configuration.
Nevertheless, you can do a --binupgrade upgrade, to be sure that configuration directory is left untouched.
In addition, for the moment, if you upgrade crowdsec the standard you will loose you bouncer configuration. Anyway, this will be fixed very soon.