This is caused by a misconfiguration with the tool.
This solution will work for both HTML and HTML pass-thru on normal fields and on Document Sets.
The following 3 items have to be true before in order for the migration to be successful
1. On the Sharepoint tab data definition: Make sure the (document set) data field is set to Note for the Target Type
2. On the Notes tab data definition: your data field has have ColumnType as Item and ReturnType as HTMLString
3. In SharePoint, the field type needs to be Publishing HTML.
Once these 3 condiditons are met, you should no longer get semi-colons in your migrated data.
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