We don't track overrides on Depth Features like we do on other fields (the small orange or blue triangles on fields of the Treatment Data page). When a Service Company uploads any Treatment Data with Depth Features after you've made changes, it may clear out whatever you had previously entered in Depth Features for all Stages.
The solution is to either have the Service Company remove Depth Features from their Treatment Data Import spreadsheet, or to wait until after they've loaded that file for all Stages to make any changes.
For more information on Depth Features & Treatment Data overrides check out the Treatment Data article!