Is it possible to overwrite an existing file in ArcMap ModelBuilder?

Yes, it is possible to overwrite an existing output file in ArcMap ModelBuilder. Follow the steps below to enable overwriting the output file:

1. In ArcMap, click the Geoprocessing menu and click Geoprocessing Options.
2. Check the Overwrite the outputs of geoprocessing operations option.
3. Click OK.

In some cases, when involving enterprise geodatabase or server connections, some tools fail to recognize the overwrite settings and return an error. This may be due to a known limitation of the software to overwrite outputs that reside in the in_memory workspace. As a workaround, save the output in a database connection instead of database server connection.