In ArcGIS Pro (2.1.2) when performing an Overwrite Web Layer function, a warning is issued stating, "If you overwrite this web layer, any popups configured or changes made to the web layer after it was initially published will be lost. This may affect existing clients using the layer by changing layer order or available fields." In my first test of this the warning turned out not be true as nothing was apparently lost.
I posted an inquiry under ArcGIS Pro regarding this and got the following response from an Esri member,
When overwriting a web layer the new layer you are publishing can have an entirely different schema than the existing layer. If the schema differs (i.e. different field names, new fields, deleted fields) than the pop-ups will be lost and need to be re-configured. If the schema is the same, then the pop-ups should maintain.
My response to this was,
I have to question the wording of the warning as it leaves no room for uncertainty. It says that configurations and changes "will be lost." I think it is alarming and, by your explanation, it is also inaccurate. At the very least, I believe "will" should be changed to "may" and, even better, a concise explanation should be included.
I believe that the warning for this function, and perhaps others related to Overwriting, needs to be reviewed for accuracy and content so that users, both experienced and inexperienced, will have the proper information to proceed with confidence in the process and the outcome.