It will have no effect on them.
The most likely effect of this will be that they'll suddenly be greeted with a 'session expired' type message and will be required to log in again.
If the customers aren't logged it, they'll suffer a 'hiccup' and basically lose anything already placed in their cart and will need to re-add them.
Then there are the unpredictable effects of what could happen if something was being done at exactly the 'wrong' time (such as midway through a paypal payment).
It should only take a few seconds to make the change. My suggestion would be to place the store in maintenance mode for the short time it takes to do this. That way you'll avoid any unpredictable surprises, and it'll be a little less annoying for the customers already on the site.
Cheers
Rod.



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