Hey @Michael_1, I believe I can help you out with this.
So, when you deduplicate accounts in Salesforce, the master is kept in sync with HubSpot, but the duplicate company in HubSpot remains. This is because the duplicate HubSpot company is trying to sync with the corresponding Salesforce account but cannot find the Salesforce Account ID anymore because it was merged with another record in Salesforce. So this is the reason why you have to handle the deduplication twice on both platforms, because the sync is effectively broken for those records when you conduct the merge in Salesforce.
Additionally, you cannot merge duplicate HubSpot companies when the Salesforce integration is active. To merge duplicate companies in HubSpot, you need to uninstall the integration, deduplicate your company records, then reinstall the integration. This is a huge pain — probably not worth it 95% of the time and there is no easy workaround.
However, using Insycle, you can deduplicate companies/accounts across both platforms, in bulk, using any data field to identify the duplicates, while keeping your sync in place. I won’t go into the specifics of how it works too much, but essentially this is done by creating a custom field, “Deduplication Master Record,” on both platforms. Insycle automatically populates the correct master record with “Yes,” and then allows you to merge duplicate HubSpot companies into that record, while keeping the Salesforce sync active.
Full disclosure — I work for Insycle. But it sounds like this is costing you guys time and money so it might be something you are interested in.
If you’d like to learn more about how it works, we recently put together a big guide on the subject of merging HubSpot/Salesforce duplicates and keeping the sync in tact (works for contacts/leads/accounts/companies), here: How to Merge Duplicates in HubSpot and Salesforce and Keep them Syncing