If you are fiddling around with your order in the checkout screen and you apply your rewards points and then decide not to checkout, the points don't come back, even if you completely exit out of the screen. So if you are debating on products or fiddling around with your order total, don't apply your rewards until you are ready to check out.
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Update to this issue - I found that when I logged back in the next day, the reward points were back to their original balance. I don't know approximately how long it took to refresh the point balance or if that could be achieved in the same day, but 24 hours later, point total was restored after not following through on an order. Good news is that it didn't disappear forever!