I am having a promblem with a mission I created. It is a battle between two fairly large fleets, and ships start to disapear about halfway through the mission. Does anyone know how to fix this or what causes it to happen?

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Race Trah will dominate the world of Ares

Are the ships actively engaged in battle? If so sometimes in a large battle ships will appear to just dissappear when they are destroyed. This is because with all the ships and weapons flying around you quickly hit the max objects limit of someting like 255 somewhat quickly.

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Ares and EV:Nova plugin writer and all around helpful guy...

Yes, they are all engaged in battle. This seems to effect the condition of no ships left. Is the only way to fix it to lower the number of ships?

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Race Trah will dominate the world of Ares

Yes
You need to have less than about 130 ojects at the start of the level. You could try creating a device which produces more ships as time goes on, rather like the asteroid shooter to get round this problem. Other ways are to modify ships so that they do not use fighters or missiles.
You need to script the battle so that you never exceed a count of about 200 objects.

My plugs "It's War" Part 1 & "It's War" Part 2 (just released) each have levels in them which push the maximum number of ships to the limit.
I too like big battles!

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Oh, so it is another bug hunt then...