Will it be safe to continue I wonder, if the current issue goes pear shaped?
As C DM pointed out, we use our credit cards outside of Apple Pay all the time. If they're compromised and we report it, we're covered by the bank with either method.
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People have gone a bit overboard thinking that they suddenly need airtight security after so many years without.
Ironically, having extra security actually can work against the consumer in rare circumstances.
For example, when PINs were stolen from hacked EU terminals a few years ago. It took a long time before banks believed that customers had not given away the info on their own. Likewise, if someone used a fake finger to buy something with your phone, you could be hard pressed to prove it was not you that your phone's TouchId had authenticated.
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The upshot is, in normal life there's no need to worry. If an exploit came along that allowed criminals to access a phone's info, it'd likely be noticed after a while, same as with other breaches, so you wouldn't be alone.