Error message
xillybus: Lost sync with interrupt messages. Stopping.Meaning
Each hardware interrupt from the FPGA to host is accompanied with information about the reason for the interrupt. This error is issued when the host driver has fatally failed to synchronize this information with interrupts, and hence it can't relate to interrupts anymore. Effectively, the driver stops reacting to the FPGA.
Error messages following this one are most likely a result of this condition.
Recommended action
This is a severe unexpected fatal condition, and it should be reported.
To get Xillybus working again, power the computer off, reconfigure the FPGA and power the computer on again.