I read some comments os.flush() or os.fsync() can be unrelated to problem. External application can be written in C# or whatever you want.

Under Windows (not Linux) - modification dates will be stalled in such sequence.
os.scandir()
dir_entry.stat() # let it be dir_entry.path == 'test.txt'
dir_entry.stat().st_mtime # will be for example 1
os.scandir()
dir_entry.stat() # let it be dir_entry.path == 'test.txt'
dir_entry.stat().st_mtime # will be STALLED for example 1


Under Windows (not Linux) - modification dates will be refreshed in such sequence.
os.scandir()
dir_entry.stat() # let it be dir_entry.path == 'test.txt'
dir_entry.stat().st_mtime # will be for example 1
os.stat('test.txt') # this code do something and it is not stalled in next call
os.scandir()
dir_entry.stat() # let it be dir_entry.path == 'test.txt'
dir_entry.stat().st_mtime # will be CHANGED for example 2