I do not think that there was about motherboard replacement. I think that was small production issue with that Librem 5 from @librem5, and that this issue belongs to the past.
Expert people from Purism you will reach by sending message to support@, where providing your purchase reference number (within one year of receiving your Librem 5, I’m quite sure). Rest of this post is just my unofficial/wild guessing, therefore please do not spend to much of your time (although you made myself awake, aren’t you, all fine with me) diagnosing if something broken, actually rely on them helping you to fix what “broken”, when something broken.
You might try to help yourself by flipping USB-C male side of currently used USB-A to USB-C cable and mark upper side if got to the point that USB communication works that way. Take another USB cable … another one until you get to the point that uuu -lsusb actually works there (provides expected output). @Flo127, what I wrote here about uuu -lsusb is not related to your post above, will come back to you soon.
Similarly, while it was about USB communication (and not about exclusive motherboard issue) you should try first to copy files (back and fourth over Nautilus) to some old-fashioned, up to 32GB, preferably USB 2.0 Flash Drive over quality USB-C to USB-A OTG adapter (if not already having some USB-C flash drive, as I don’t). Is it some USB Flash Drive or USB-C SD card reader mounting there at all?
If above doesn’t work on your Librem 5 you should (probably) follow advice in this post: External battery charger for Librem5 - #83 by dos.
EDIT: Although perhaps USB-C motherboard (bottom one) indeed replaced: