Actually I just rethought my problem, and it's been revised slightly. Here's the gist of it now:

mirc1 is connected 24/7 to a static set of channels and servers.
mirc2 is dedicated bot client that is connected to the same channels on only one server.

ServerA is the server in common between mirc1 and mirc2. All channels are assumed to be hosted on ServerA. ChannelA will always be connected to by mirc2. ChannelB will contain userA that the mirc2 bot will join/part on UserA's quit/join message.

So..

mirc1 sees UserA quit (disconnect, netsplit, etc).
mirc1 fires trigger telling mirc2 to join ChannelB
mirc2 takes over bot functions in ChannelB until UserA re-joins.
UserA re-joins ChannelB and mirc2 fires trigger to part ChannelB.

I hope this makes some semblance of sense.