I’ve had this happen a few times as well on multiple different missions. Sometimes I can still complete the mission (with a pilot deviation), but sometimes the sim will stop tracking my progress all together and I have to restart the mission. If it happens, it’s when I try to use the ATC window for related functions instead of the D-pad shortcut, but does not happen all the time.
One possible workaround that I’ve found is I can click the COM 2 tab in the ATC window and get back in contact that way, but sometimes it will cause a flood of missed messages to come in and result in multiple deviations.