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I haven't directly but I just happen to be staring at Pivotal Tracker which handles it pretty nicely. The do as you say and push a little lightbox which says "A system change has occurred requiring a refresh of this page. Please click 'OK' to reload Tracker."

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And Gmail would have the same problem. But to date, I have never seen Gmail ask to refresh..

I think how Gmail handles the problem is they keep multiple instances of the server-side software running, one for each version of the API. From my experience, whenever GMail rolls out a new feature, I don't see it until I do a refresh and frequently that's what GMail tells me I need to do to see the new feature.

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