Ok, I've made some research about crashing on a converted map:
The event is caused by Redpower2, not sure why, but it seems to be caused by buffers.
Redpower2 machines have a buffer (an imaginary inventory that can store millions of items if there's no where for them to go.
For example: You have a high frequency timer (thrice in a second) attached to a big line of block breakers. These block breakers are in a cobblestone generator. This would cause a massive amount of items traveling trough pipes that obviously can't keep up with the pace. Resulting a situation where these block breakers a re producing more and more cobblestone, but they have no where to put them. so in that case they will store the items inside them (in the block's buffer (a.k.a. it's imaginary inventory that can hold an unlimited amount of items))
Of course the machinery doesn't even need to produce this much items, but this is a one way to reproduce the problem.
When the map is converted, every single time a machine that has items inside the buffer. The game will crash for a reason that goes usually like this:
com.eloraam.redpower.machine.HandleItem.
Normally this wouldn't be such a big deal, but we are dealing with a big multiplayer server map wich has a ton of bad machinery. Without a good solution we can't keep this map. Is there any way to empty every block's buffer inside the server.
Here's an error report caused by a bad machine. [Pastebin]: http://pastebin.com/XGjJWr7D
I'm looking for any solution that could save the map. A way to remove blocks in certain coordinates. (pos1:x,y,z - pos2:x,y,z | //set 0 - Isn't it strange that worldedit doesn't have this kind of function)