Just came across to an interesting research on the Islamic fighters, recruited by Azerbaijan, during the Nagorno-Karabakh war with Christian Armenia in the early 1990s.
Speaking of the number of the Islamic fighters, researcher Micael Taarnby writes:
Whatever the true number of Mujahedin, even the most conservative estimate of around 1,000 represents a considerable influx of foreign fighters. Unlike the parallel situations in Bosnia or Chechnya where individuals or smaller groups of foreign fighters made their way into the theatre of war, the scale of operations in Nagorno-Karabakh required a very different logistical setup, complete with a sizeable airlift capacity. The foreign Mujahedin were flown in on chartered civilian aircraft and this considerable traffic resulted in the joking reference to an unknown company called Afghan Airlines.
Ironically, according to the author, the Afghan fighters had more respect for their Christian Armenian enemies than for their Muslim Azeri bosses:
In spite of the official Azeri position that Afghan Mujahedin did not exist, such individuals were easily spotted in tea-shops in Baku because of their tribal dress and full beards. Apparently discipline broke down occasionally, even requiring young Azeri conscripts to be moved to other sectors of the front to avoid their killing by the Mujahedin. Insubordination became a problem, probably because of two characteristics specific to Afghan Mujahedin: fearlessness and the concept of loyalty. Apparently they cared little for their Azeri relations, who were considered inadequate paymasters and poor soldiers but also, and perhaps even worse, as only nominally Muslim. They did, however, respect their adversaries, the local Armenian Karabakhis, who had an intimate knowledge of the terrain and the ability to exploit this advantage on a tactical level. Often the Mujahedin would find themselves outmanoeuvred or fired at from multiple directions, not even knowing where the enemy was placed.
Speaking about particular involvemenet of the Afghan fighters, the author writes:
Many atrocities were committed during the conflict, including decapitations and the ritual mutilation of civilians, although it is not known what role the Mujahedin played in this respect. However, their presence at the frontline and the style of fighting reminiscent of the Afghan theatre increase the possibility of their involvement. Eyewitness reports have confirmed that villagers had had their heads sawn off by advancing Azeri troops, although no unit identification was presented.
Where did the fighters go after the war? Mostly to Chechnya, since Shamil Basayev – the Chechen Islamist fighter – was himself fighting in Nagorno-Karabakh.