Here is what I have noticed ( we sync with Lansweeper ).
The template upload overwrites and the sync will append. ( there might be an option that determines this but I am not sure )
I.E.
1. We made an initial asset sync with Lansweeper
2. We updated assets with a template data import, this overwrote the Lansweeper data, only on the fields that were being updated in the template.
3. On the next Lansweeper sync, the Lansweeper data appended it's data that was removed by the data import to the data from the data import.
I think you need to test ( try a data import on just one asset ) and look/note the WHD options carefully.
Also consider updating the attribute mappings you set in WHD with your SCCM sync, that could be helpful during an import or sync depending on what your goals are.
Also note that when you download templates you get a slightly different template based on the client key you select ( username or email ).