@katherineladue It sounds like you need to some excel manipulation here - the Record ID that you are exporting is likely the HubSpot record ID and not the SFDC Account ID.
If you export all companies in the CRM with Account ID (Salesforce), and Record ID (HubSpot), then sort from A > Z by SFDC ID on the export AND the activity file, you could combine the sheets and re-import it.
Ensure that you’re mapping to Record ID with your companies in the multi-object import.
Let me know if you have any questions.