Update:
I reinstalled MainsailOS, I am using another SD-Card and another Raspberry Pi 4. I also switched from OrcaSlicer to PrusaSlicer and again, I got the “Timer too close” error. Taking every failed print into acount it seems like I am getting these errors after about 35 minutes every time.
Finally, I switched from UART to USB for my main MCU, the Fysetc Spider V1.1. The print (sliced the same object but again with OrcaSlicer, 4:40 hours print time) finally finished. 
Thus, it looks like there is a problem with the UART connection. I don’t know if it was introduced through system updates or Klipper updates. However, this is still a guess and not verified, but I hope the issue is gone forever and won’t appear again …