Coming from Nintendo's own FAQ...

Q: I have used Nintendo eShop in different regions, and I have funds in multiple currencies in my balance. What will happen to these funds after I register a Nintendo Network ID?

A: After registering a Nintendo Network ID, you will be unable to change regions and use multiple currencies – for instance, pounds and euros – in Nintendo eShop. The funds in the currency that corresponds to the country setting of your Nintendo Network ID will remain, and any funds in other currencies will be deleted and no longer usable. Please make sure to use up any other currencies before registering a Nintendo Network ID to your Nintendo 3DS system.

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Looks like Nintendo is out to stop those that have been switching regions to take advantage of deals. Thanks to Kolma for the heads up!