These Eagle project files were downloaded from arduino.cc and had been modified. The original .sch file is incompatible with newer version of Eagle. Text replacement is needed for upward compatible.
- Download this zip and unzip.
- Open Eagle, then "Open"->"Text..." to select NanoV3.3.sch file from the unzipped folder.
- Saving after "find-and-replace".
Tested on Eagle 9.6.2.
Credit to ktnewcom from element14 forum.