(Fortunately I am not among the affected passengers)
There are protests being held in Hong Kong International Airport right now. In response, The Airport Authority closed all check-in counters before evening. Unlike Monday, where all departure flights at night were cancelled, only a handful of flights were cancelled today; a majority of them are departing on time with transit passengers and cargos only. It is said that passengers who are not checked in before the check-in counter closes prematurely, would be treated as no-shows.
To make this question more general, consider a flight from non-EU airport to an EU airport, operated by a EU airline. This flight is covered by EU rules regarding delayed and cancelled flights.
A passenger of that flight arrived at the airport well before the check-in deadline. However, the check-in counter for that airline was prematurely closed even earlier (or was never open to begin with). This may be caused by protest, ground staff on strike, or other reasons beyond the airline's control. The airline decided to get the aeroplane in the air on time, without that passenger on board. Is that passenger eligible for compensation under EU rules?