All settings for payment types were deleted. Luckily I tested it on a dormant system. Took ages to find Paypal API signatures and had to re-enter order confirmation and payment details (and not sure they are as they were). And still need to test the system. Had this been done on a live shop it would have meant the site being down for hours until being brought to my attention. For the remaining sites I will make sure these are copied first before upgrading. Any other gotchas to look out for?