In my model builder I use the merge tool with the field map to reconciliate the fields of the two data source. Problem is: When I set the field map, validate by clicking ok and reopen the tool, if I click to change anything in the tool, the field map reset. Even if I change the output field name, the field map reset.
I wonder if it is a common issue or it may be related to my model. I consider using the Append tool to replace this or even some Calculate field, but would rather keep the Merge.
I am currently experiencing the same thing. I started creating a set of models a few months ago. Some of the input data has changed so I've had to re-map fields in my Merge tool. I add and map 9 new fields, click ok to accept the changes and run my model. The GP tool following the Merge tool fails and says that a field does not exist within the table (ERROR 000728). When I open the merge tool in the model again the 9 fields that I mapped are no longer there.
I had the a similar issue when using Merge with inline variable substitution in files paths. The only workaround I could find was to replace the variables with hard-coded paths (unfortunately).