If you have all the board expansions but sometimes don't want to use all of them (maybe you have fewer players than usual), what portions of the missing expansion(s) do you leave out?
The rules seem to be pretty liberal on this subject, basically saying that it's fine to use parts of an expansion, but not all of it.
Some changes seem to be pretty obvious: it doesn't make much sense to keep a missing expansion's Mythos cards, since they will constantly be referring to unavailable locations; if you're playing without Dunwich or Kingsport, of course you need to remove the gate markers for their Other Worlds; but virtually all items are usable in any game, and I suspect that pretty much everyone who has Dunwich always uses the Injury and Madness cards.
When it comes to Allies, however, the situation is unique. Obviously, the simplest way to deal with them is not to include those from a missing board expansion in the deck when you select the 11 availables during Setup. Though reasonable, this solution may not be particularly desirable, especially if you'll be missing all those wonderful Kingsport Allies. The problem with keeping them in the deck, of course, is that the overall probability for your Investigators to gain Allies will be significantly reduced without the chance to have encounters at the locations that reference them by name. Following is a (highly unofficial) procedure we've been using to cope with this dilemma.
All Allies from the missing board expansion (hereafter referred to as Homeless) are included in the random draw during setup. When the players review the 11 choices to see which ones are available, the number of Homeless is noted (if no Homeless were drawn, there is no need for this modification) and a number of additional Allies equal to the number of Homeless is drawn from the remaining unchosen Allies. These additional Allies are called Subs (note that if other Homeless are drawn in this process, they must be replaced by drawing other Allies whose home boards are being used in the game). These Subs are kept in a stack on or near the Arkham board, and any player may look at the stack at any time.
After starting the game, the usual rules for Allies apply, except that whenever an Investigator has an encounter referencing a Sub by name, he may obtain that Ally by whatever means the encounter specifies. Whenever this occurs, a random Homeless Ally is removed from the deck of availables and is returned to the box (with the deck of availables reshuffled). The Sub has now permanently taken the place of that Homeless in the group of 11 availables for the game.
Similarly, if an Investigator gains a Homeless Ally by means of any normal game effect (items, encounters, Boarding House, etc.), a random Sub is returned to the box, and the Homeless Ally obtained cements its position in the group of 11 availables.
Game effects that enable Investigators to obtain Allies that have been returned to the box (for example, Charlie Kane's (KH) Connections ability or The Bureau's (MH) Protective Custody feature) do NOT apply to Subs or Homeless that have returned to the box as a result of this modification--such effects apply only to Allies returned to the box by normal game effects.
Allies from either version of The Curse of the Dark Pharaoh expansion do not suffer from a significant drop in their probability of being obtained when any expansion boards are missing. Therefore, they may serve as Subs but not as Homeless.