Issue
When you are synchronizing Microsoft Office documents between two SharePoint libraries that contain managed metadata fields, it can happen, that the metadata values in the target are not set to the correct values.
Background
SharePoint document libraries and Microsoft Office documents are strongly integrated. The property values of a document are extracted and written to corresponding columns in the SharePoint library. When SharePoint library metadata is set for a document, the value is also stored in the matching document property.
For managed metadata and lookup columns, the related values in the document properties are not stored as plain text but as a string that consists of an Id, the actual string value, and, in case of managed metadata, the Id of the parent term set.
If a document contains such a property and is synchronized to another SharePoint, the Ids no longer match the new term store id or lookup list id which leads to an issue during propagation of the document property value to the SharePoint library columns.
Resolution
As this issue is caused by an integral SharePoint/Office documents feature, the Cloud Connector is not able to work around it. However, it is possible to disable the SharePoint SPWeb Property Parser which controls demotion and promotion of document properties in SharePoint libraries.
A description, of how to disable this parser can be found here: SharePoint SPWeb Property ParserEnabled
Note: In SharePoint Online it is not possible to disable the parser at tenant admin level. You need to open a support case with O365 support team (parserenabled in sharepoint online).