Many times I find myself saying thanks to a store clerk, flowed by their saying thank you very much. I am used to walking away saying bye or have a nice day, but am not sure what the equivalent is. What is the proper phrase for someone I don't know but a polite have a nice day. If this isn't common to do that is also good to know.
It isn't common, especially in those mass selling stores. Not I'm highly introvert, but most Japanese don't say anything, or just nod a little (which is a slightest form of bowing).
Of course, they do usual greetings as friends when the clerk and the customer have personal acquaintance (which is pretty often in my neighborhood store), but in most cases, the Japanese in-store conversation is the clerk unidirectionally greets the customer.
However, if you'd like to say something in response to clerk's ありがとうございました,
should not sound very weird, or in restaurants,
makes you polite.
In some one-man managed small shops or boutiques, you might feel the real necessity to say a word like:
さようなら, また来ます, またよろしくお願いします etc.
but in my opinion this sort is nothing but general social conversation.
To give you an idea of what is normal in case you are not familiar,it's kind of strange if the customer doesn't know the clerk personally and still responds in an extra friendly manner. (which includes saying something like "have a nice day")