Adam
Those logistical issues stated above make sense, I am going to assume land is not a problem, and that there is a financial incentive for the club. Maybe this would allow for the addition of a large block of new members, or relieve an already overused 18 holes, whatever.
My home course was built in the 1920's with 27 holes designed and built all at the same time by Toomey and Flynn. During the Depression or the Second World War the club ceased maintenance on one of the nines. In the mid-90's a group of members formulated a strategy to rebuild it as close as possible to the original (two holes required alteration due to current driving range). This nine was chosen to be 'let go' due to a geographical disconnect with the other 18 and so, in the name of being efficient, that simply made the most sense. Wayne might have an aerial that could be posted to illustrate if he checks in here.
Now that the C-nine has been back in play for about 7 years I would recommend a couple of ideas;
1) To avoid the "no one course" problem, just let the architect you choose know that you want one nine separated from the other two geographically so there is a clear flow of 18 holes.
2) Begin the third nine with the intention of utilizing it for ancillary golf functions (ie: outings, juniors etc..). But make sure it can flow with the other two nines so that a rotation is not an issue at certain times. This eases the transition during heavy maintenance periods and such.
Good luck