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You should probably take a good look at your game and work out why you would need 999 maps; you could probably condense them down, for example by making all of the generic house buildings in a single town share the same map.
Here's a 'disc changer' script, but be warned the thread is from 2008 so it might not be supported any more. Essentially how it seems to work is that you have multiple projects, each of which can have up to 999 maps.