I'm still a little puzzled about why the 2 second retry doesn't work. It might be worth diving in deeper to figure out why the data received during the retry never makes its way back to libusb. It's a bit of an edge case, but it seems like it could potentially be a bug. I might consider bringing that up as a question on the linux-usb list.
As a side note, I want that reasonably priced <https://github.com/ataradov/usb-sniffer>.. I've felt the need for one several times (I've always enjoyed work which involves looking at problematic low level traffic data, for some weird reason). But soldering a QFN chip is not something I'm set up to do, unfortunately. However, apparently AliExpress sells them pre-built.. though Taradov himself states "Do not buy CY7C68013A from eBay or AliExpress, they all are either fake or sketchy". I wonder if that also applies to pre-built boards including that MCU.
The sketchy part comes from no buffering/clamping/conditioning of inputs on those $5 "logic analyzer" ebay boards. Means you only get CMOS compatible signal levels* and might fry it with bad signal, but at prices like this https://pl.aliexpress.com/item/1005003649856071.html blowing a few is a non issue.
* meaning you need to know your probed signal will work beforehand, for example by verifying with a scope first.
but as usual, the Internet Archive saved the day.
So many times, when working on hardware of only 10 years ago do you hit this wall of “resource no longer available”. And often archive saves the day.Consider donating if they helped you.