Together with Johannes I secured that this was not an error in the Core but an issue with the hardware or driver installation in Windows. After some extensive searching I was able to find a solution to the problem, although we could not find the cause.
If you should experience the same issue: In Windows 10 move your mouse over the windows logo in the left bottom. Right click and choose Device manager. At the bottom you will find under USB Device's "Axoloti Bulk Interface". Right click and choose Remove hardware. Disconnect your Axoloti and after a few seconds reconnect it. In my case the problem was gone and the Core was again fully operational.
Note: I had to translate the menu items from Dutch so please be aware that text in English or your local language might be (slightly) different.