Hi!
When you run a script in Thonny, be it on local disk or on Pico, Thonny makes soft reboot in raw mode (ie without running main.py) and sends editor content to MicroPython REPL. I believe soft reboot does read something from flash, but submitting code to the REPL shouldn't.
If you want more confidence or more details, then I recommend asking at MicroPython forum.
Best regards,
Aivar