vincebodie
Hi
The avatar does not removed on updates, If you are updating from 4.5.8 to 4.5.9 , you just need to download the latest version and install it on your site.
About the customization i am not sure what custom work you applied, If its in the template override it would not be override.
Otherwise you need to take backup of your all custom changes file and re apply them on new version.
Do not forget to take backup of site before updates. Also, we do not suggest core hacks in Jomsocial as it can break site if the custom changes are wrong.
Regards