I have had problems writing to the onboard filesystem from Windows. I sometimes see complete filesystem corruption, and sometimes just problems with one file. See https://forums.adafruit.com/viewtopic.php?f=60&t=109687 for background.

Specific scenario, showing a file that CPy has trouble reading:

The file in question is here: main.py.txt. (Renamed from main.py to main.py.txt so that GitHub will take it as an attachment.) I wrote this Python code while doing some CPy I/O testing, and the specific code probably doesn't have anthing to do with this problem. However, this file is 556 bytes long, so it's more than one 512-byte block, which does seem to be important.

If I write this file to D:\CIRCUITPY\main.py using NOTEPAD.EXE, it runs just fine. It prints "5" and the button-reading loop works.

If I write this exact same file using Notepad++ (a very common lightweight editor used on Windows) it does not work. The serial port shows:

Auto-soft reset is on. Simply save files over USB to run them.
main.py output:
Traceback (most recent call last):
  File "main.py", line 26
SyntaxError: invalid syntax

Line 26 is right around the 512-byte boundary in the file.

In the REPL, I can read the file I wrote with NOTEPAD.EXE:

>>> import uos
>>> uos.listdir()
['System Volume Information', 'main.py']
>>> f = open('main.py', 'rb')
>>> chars = f.read()
>>> chars
b'import nativeio as io\r\nfrom board import *\r\nimport time\r\n\r\nled = io.DigitalInOut(D13)\r\nled.switch_to_output()\r\n\r\nswitches = [io.DigitalInOut(pin) for pin in (D6, D10, D11, D12)]\r\nfor switch in switches:\r\n    switch.switch_to_input(pull=io.DigitalInOut.Pull.UP)\r\n\r\n\r\ndef blink(n, interval=0.2):\r\n    for i in range(n):\r\n        led.value = 1\r\n        time.sleep(interval)\r\n        led.value = 0\r\n        time.sleep(interval)\r\n\r\nprint(2+3)\r\n\r\n\r\nwhile(True):\r\n    for i, switch in enumerate(switches):\r\n        if not switch.value:\r\n            blink(i+1)\r\n\r\npass\r\n'
>>> f.close()

But if I write the same file again with Notepad++, I get an OSError when trying to read it in the REPL:

>>> f = open('main.py', 'rb')
>>> chars = f.read()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
OSError: 5

I can TYPE either file from CMD.EXE, and if I use od (from GnuWin32) to look at the characters in the file, they are identical.

I have repeated the cycle of writing with NOTEPAD.EXE and then Notepad++ and I consistently have the error only with Notepad++. Once or twice TYPE complained it did not have access to the bad version of the file, but I cannot reproduce that problem consistently. If I look at the file properties in Windows Explorer, the two versions have identical properties and sizes.

I've looked at the Notepad++ source code where it writes files. It looks innocuous: it uses ::fwrite(). It does support UTF-8, but the file in question is all ASCII, and I set up Notepad++ to write it as ANSI.

This appears to be some oddity or corruption about how Windows is writing to the CPy filesystem. I've inquired on the Notepad++ forum about whether it does anything unusual when writing files, and will report back if I hear anything.

The workaround is not to use Notepad++, but it seems important to figure out what's going wrong so other users will not have the same problem. I did some websearching and haven't turned up any similar reports about Notepad++, FatFs, or MicroPython.