I have a Framework 16 with a Ryzen 7840 that I plugged a broken USB adapter into a couple of times without realizing the problem. Now half the expansion ports aren’t working reliably or at all. I have an electronics background and was wondering if maybe replacing a SMT fuse was likely to fix it or if I’d have to get a new mainboard.
Moving the expansion cards doesn’t change anything, the same slots remain inoperable.
Running Windows 11 25H2 (not that this is relevant).
Sorry to hear that half the ports are not working as intended. Sometimes the EC marks ports as invalid to protect the system if a shorted or defective device was plugged in. A few users have reported that resetting the mainboard, physically disconnecting the battery, and then bringing the system back up has sometimes reenabled ports that were not working properly. Consider contacting support though for the best guidance. We are all end users here on the forums.
Let us know how it turns out. 
I have done this USB port fix a couple of times too. But my old machine had CMOS battery so I could remove it. Not sure if removing the main battery would delete you bios settings as well? I guess you will find out 