Error upgrading old prefix (Game: Planetbase – 403190)

This game ran fine a few years ago, now it doesn't start

Proton: Upgrading prefix from 3.16-1 to 6.3-3 (/home/johannes/Steam/steamapps/compatdata/403190/)
Proton: Removing old xinput registry entries.
Proton: Removing ShellExecute DDE registry entries.
Traceback (most recent call last):
  File "/home/johannes/Steam/steamapps/common/Proton 6.3/proton", line 1264, in <module>
    g_session.init_session(sys.argv[1] != "runinprefix")
  File "/home/johannes/Steam/steamapps/common/Proton 6.3/proton", line 1078, in init_session
    g_compatdata.setup_prefix()
  File "/home/johannes/Steam/steamapps/common/Proton 6.3/proton", line 649, in setup_prefix
    self.migrate_user_paths()
  File "/home/johannes/Steam/steamapps/common/Proton 6.3/proton", line 623, in migrate_user_paths
    merge_user_dir(src=old, dst=new)
  File "/home/johannes/Steam/steamapps/common/Proton 6.3/proton", line 102, in merge_user_dir
    try_copy(src_file, dst_file, copy_metadata=True)
  File "/home/johannes/Steam/steamapps/common/Proton 6.3/proton", line 123, in try_copy
    shutil.copy2(src, dst)
  File "/usr/lib/python3.7/shutil.py", line 263, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/usr/lib/python3.7/shutil.py", line 120, in copyfile
    with open(src, 'rb') as fsrc:
IsADirectoryError: [Errno 21] Is a directory: '/home/johannes/Steam/steamapps/compatdata/403190/pfx/drive_c/users/steamuser/My Documents/Planetbase'

Start in the Proton script at migrate_user_paths(), then follow merge_user_dir() and try_copy(), which the traceback identifies as the failing path. Reproduce the upgrade for compatdata/403190 and verify that a directory such as My Documents/Planetbase is handled without IsADirectoryError and the prefix upgrade completes.