During the auto-sync, the most current version of an account's data is copied over to Zoho Invoice. So any changes or additions that are done in Zoho Invoice will be over-written. However, if the fields in which you had entered information are not available in Zoho CRM, like the custom fields; then they will not be over-written. Here's a list of fields that are over-written during the import.
Zoho Invoice FAQ