Note - this article is largely speculative....
'Desync' is considered to be one of the key indicators of the quality of online gaming. However, its meaning is poorly understood in ArmA. In general it can be understood as a measure of how 'out of step' clients are with the server. Eg, if a client is slowed down to the point where its simulation engine is running at a different rate to the servers, there will be desync.
The following posts from Suma may offer some insight into how desync is measured and what can cause it:
"For bandwidth control the game needs to know approximate frame duration, so that it knows how much information it should try to send in one frame. What we do is we ask rendering subsystem to tell us average fps for last 16 frames, as this is something rendering already knows. Now the problem is on the dedicated server there is no rendering done at all, and the fps returned by the rendering subsystem is wrong - often numbers like 5 seconds are returned when in fact server is running at 50 fps. We will fix this by not relying on rendering when quering fps for this purpose. We are convinced this fix should not only greatly reduce the JIP caused lag and desync, but hopefully improved bandwidth control and balancing overall."
"[desync number] is a kind of metrics of "out-of-sync" status. The smaller, the better.