777fly, i had similar experience especially in the CIS countries and China.
To answer some of you questions: for repetitive flights; series of charter or permanent regular flights (which are subject to bilateral governmental agreement) the operator has to seek for permission from its own CAA and the CAA of overflying territory and the intended destination through the diplomatic channels 45 days before intended operation. Its called form R. After receiving the overfly or landing permission (the appropriate permission numbers to be carried aboard) the operator files either RFP or makes individual request for single flights. That's preliminary work, before the actual operation begins and the flight plan for each flight is filed 1 hour before departure, which is supposed to be submitted throughout the intended route and each ATC unit has received the details at least 10 min before entry of the A/C. Its ICAO standard. In certain countries including CIS, China, Iran; Mongolia and nowadays in Europe as well, all the civilian air traffic movements are coordinated with air defence. This particular fact makes it almost impossible to reroute, while being down the route. (not in Europe of course, but absolutely impossible in China, Russia, Mongolia). That's why departing from eastern airdromes you have to sign a dispatcher clearance as well, without which its a no go. ATC departure clearance should specify the clearance limit; saying "cleared to ZZZZ .......", which means all the coordination work has been done and the ATC units are informed and overflying or landing permission is obtained. Even if you select 7600 on your box and entered the airspace without clearance you will be intercepted and probably forced to land. Absence of SSR doesn't mean the military radar doesn't see you (their primary radar is very very accurate and they do track you all the way), especially in northern China, where sometimes, outside the VHF coverage, you will suddenly hear a voice on 121,5 saying to you that you are 2,5 NM left/right of track and give you heading to re intercept the track. All in all its a dangerous game, trying to fool on ATC with tricks like loss of comm. I am afraid there are not many options for rerouting, flying in those parts of the world. Its pain in the ass being confronted with such a problem down the route, but it does happen quite often and not always resolved in operators favour.
Cheers.
