Disconnecting the two boards turned out to be much easier than I thought. The hard part was to resolder the SMD mounted micro-B USB female because its 5 pins were partly covered by the case of the connector. I bought a very thin USB soldering iron and exploited the fact that there is usually enough melted tin on the tip to create sufficient contact.
On the one hand, I praise Matias for using quality connectors between the boards. I connected and disconnected the two boards several times without issues. On the other: in my opinion, micro-B USB female are not a safe choice, except when they are located on the bottom of the keyboard and the cable is routed and blocked. Also, the connector Matias used has only two legs instead of four. I acknowledge that they designed the part of the case that encloses the connector in such a way that it absorbs much of the force. In my case, maybe there was enough play to break the contacts.
Did you end up fixing it then? I have done one of these repairs to an older Matias mini board that I purchased in that condition, although I actually replaced that connector entirely with a beefy female aviator connector that I mounted to the case. With mine, most of the pads were lifted so I had to do as tp4 described and scrape the solder mask off of the traces to tap into. I covered all of the repaired connections in high temperature hot glue, so it should be indestructible now.
I don't know if it is something that they normally do, but I have been able to purchase a parts board from Matias very cheaply. They charged me $10 for the board and $15 to ship it to me in the United States from Canada. The board seemed, to me, to be working perfectly. It was just missing caps and stabilizers. Worst case, someone could possibly pick up one of these from Matias and just swap the controller.
You probably have one of the older boards that had nothing at all reinforcing the micro USB connector. I don't know when the revision was made, but newer boards have a huge plastic block screwed into the controller that locks the micro USB connector down from every angle, which I imagine resolves this problem entirely ... since it seems to have been a common point of failure in the past.
I have
a thread on the subject, along with some easy modifications that can be done to these boards to change layout and LED colors.