When upserting an existing document, cloud squidex replaces the full document, instead of updating.
The documentation states:
The data of the content to be created or updated.
The expected behaviour for an update would be to change only the updated fields.
Yes, but this is a misunderstanding. It is either update or create. You are looking for patch.
The upsert command is used for bulk operations, e.g. imports done by the CLI and the expectation is that the final data is like the source data and a patch operation could not guarantee that.
Hey Sebastian, thanks for the quick answer. 
If that is the case I feel like the documentation should be worded slightly different. Update feels a little misleading.
Btw, PATCH is exactly what I was looking for!
Thanks