I have never heard of this kind of issue. If you are uploading Simple Products only the Simple Products' information will be updated. It's tough to update Configurable Product details (including which products are assigned to them) but it can be done relatively hassle-free using and the Configurable Item Processor plugin.
Just uploading a CSV via Dataflow Profiles or Import shouldn't unassign simple products from configurable products if the data in your CSV is just a list of Simple Products.