Ah, since a netsplit is not affected by a +l, +k, or +i, as Rock said, then you have nothing to lose about setting those modes.
The only thing you don't do is /kick. Efnet #mIRC has that problem with Modoc's script during a netsplit. So set those +l <Number>, +k, or +i modes, and don't kick anyone, then use artificial intelligence to kick out those that were not part of the netsplit.
And if you asked me, I would say +l <Number> is the best, so you could allow *some* users to join.
-Neal.
