Follow-up Comment #6, bug #34339 (project avrdude):

> This is an issue in avrdude (usb_libusb module) caused by avrdude
> resetting the USB when it closes certain USB devices.

No, this is wrong.  It primarily happens since these _devices_
disconnect from and reconnect to the bus when saying good-bye
to them, and as such, it also happens on FreeBSD.

The additional reset by AVRDUDE is supposed to be required on
at least some Linux systems for a correct function, for
unknown reasons.  (FreeBSD initially didn't have a user-
visible host-initiated reset in their USB stack at all,
and never experienced issues beyond those caused by the
devices disconnecting themeselves.)

The exact time required to see the device again is highly
OS-dependant (it's the time the OS needs to walk through all
of the enumeration process).  It can be much less than the
3+ seconds you are claiming.

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