Logic hooks that are written in the custom folder are meant to be upgrade safe. However, when I upgrade my suiteCRM, the logic_hooks.php file for Accounts and Contacts (maybe others, not sure) are written over. I did put my logic hooks in the custom/modules/ folder, and the logic hooks files that I made are there but they’re not declared in the logic_hooks.php file anymore. I suspect this is because suiteCRM implemented the google maps functionality using logic_hooks. But there is currently no way that I know of to make upgrade safe logic_hooks for Accounts or Contacts. Is there somewhere I can submit this as a report of a bug to suiteCRM?
Yes you are right. the logic hooks and the entry points are overwriten this is something we are aware of. There is a another way which is not overwriten for both of these.
You can use extensions dir to ensure they are kept upgrade safe.
you can get more information here.