I've kind of had this issue for the last few versions of ArcGIS Pro. When trying to perform an operation such as Append or Merge that uses the field mapper, the field mapper doesn't retain the modifications that I specified. For example, if I change a field from "Prefix" to "ROADPREDIR", when I click away the mapper reverts to "Prefix".
To work around this, I've had to use the Alter Field tool for each field that I'd like to change when migrating data. I'm not sure if this is a bug or what. Just putting this out there.
Are you using python scripting to perform this field mapping?
Does the same operation work as expected in ArcMap v10.x (whatever you have)?
Current I'm using the Feature Class to Feature Class GP tool in Model Builder, but this occurs when using Append or Merge tools as well. I'm not having this issue in ArcMap Model Builder.
This sounds like an ArcMap/Pro equivalency issue (There are a ton of these). I would start a case with ESRI technical support so they can research and replicate this issue themselves and send it to the development team if it needs to be fixed.
Sounds like you might be running into [BUG-000119680: In ArcGISPro, when the Append tool is used in ModelBuilder, creating variables for the input and target parameters and setting the Schema Type to 'Use the Field Map to reconcile schema differences' do not map the attribute fields.] but if you want to make sure (and/or be attached to it) you should get in touch with Support.
Thanks for letting GIS endusers know this is a bug.
Thanks for the feedback. I'll contact ESRI support about this.