When the clock connected to the Debug Hub stops running, the following error message can be observed while trying to connect to the Debug cores:
Vivado automatically picks a clock for the Debug Hub, how can this clock be changed?
In future releases, an option will be considered to manually change the clock connected to the Debug Hub.
Until then, the temporary work-around is to change the clock connections using the following Tcl commands:
set DEBUG_HUB_CLK_PIN [get_pins dbg_hub/XSDB_CLK_I]
disconnect_net -net [get_nets -of $DEBUG_HUB_CLK_PIN] -objects $DEBUG_HUB_CLK_PIN
connect_net -net [get_nets <continously running clock net name>] -objects $DEBUG_HUB_CLK_PIN