The (emulated) HW clock is important as it gives the OS a time during startup (can be set manually if needed: RTC start date parameter). While an OS is running, it is not relying on the HW clock but will use the "system clock".
You can sync the time between the HW and system clock in either direction with the hwclock
tool under Linux.
Once the VM is booted, there should not be any interference with the VMs clock from the hypervisor side.