The src subfolder of the sketch folder has the special property of supporting recursive compilation. However, when you use File > Save As... with a sketch that has a src subfolder the sketch folder at the new location does not contain the src folder from the original sketch.

The Arduino IDE already handles Save As for the data subfolder so it should be easy to handle the src subfolder the same way. This PR may serve as a helpful reference: #6041

Related: #10931