When onboarding with Intercom, we ended up using the defautl zendesk import, which misassigned a lot of companies and users. Later on we used the API to reimport Zendesk tickets, companies and users, however it turns out that ‘deleted’ tickets still appear in reporting.
We’ve also had an issue where a product bug in our product caused several thousands emails to our support inbox. We also deleted these tickets. However this now means that we have to jump through hoops to get accurate reporting.
By default any deleted conversation should not have an effect on reporting.