Ask HN: How do you inform clients about unforeseen costs?

I've been running a digital agency for about 3 years, and things are going well, but I've always had trouble communicating to clients about additional unforeseen/unquoted costs.

A recent example was when a client wanted to simply update the icon for an app in the Apple/Android app stores. Simple enough, so I quoted it and started the process. We used PhoneGap (don't say it!), so any new app submission required us to upgrade to the latest version of the framework (due to a critical security update). Which would have been fine, but some of the plugins we used are not yet compatible with that version. In this scenario, we would need to rewrite the plugins to work with the new version, or remove the functionality associated with that plugin.

In this case, we're dealing with a non-profit organization that doesn't have deep pockets, and we're small enough to take a hit from additional free labour (that we're already putting in to a certain degree).

Name your reason: it's PhoneGap's fault, or poor management of expectations, "you should have r&d'ed more before quoting, budget, etc. They're a lot of low-hanging (good and valid) reasons to pull from - but it doesn't seem to make a difference what I try to prevent. I feel real shame in not being able to articulate to a point of absolutes.

Once you put a project down for a while, it's hard to remember exactly all the reasons for its appeal, functionality and state.

How do you manage expectations, and if it isn't absolutely possible to do so, how do you prepare the client for bad news about additional costs, or the possibility of not being able to complete the request?

Thanks!