I hope this is just a support question and not an idea (though will happily move it if so). I've found that when using Layer Masking in ArcGIS Pro, that if I then move/reorder layers with a Mask setting applied (i.e. Land Systems (FPC) in the image below) in the table of contents, it wipes the mask setting. Likewise, if I move a layer that is being used as the Mask (i.e. Operation Mask in the images below), layers masked by that layer lose the setting and need it reapplied.
Table of Contents;


Hope that makes sense!