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How many miles are on your motor? You don't want to put fresh tight heads on a high mileage motor. But the answer to your question is no it doesn't mess your block up taking off the heads as long as its done properly. You would need new hardware when installing new heads however. Your old head bolts will be stretched
Ok when doing a head swap on a high mileage shortblock its critical to run a compression check on the cylidners to determine the condition of the rings. When you have an overall high mileage motor and the rings have some wear along with the components of the head and valve train, putting on a fresh set of heads with a fresh valve job often be the nail in the coffin to a motor with lack luster compression due to worn rings. Thats what people are referring too when they say "it can mess up the motor", if your compression checks out strong there are no worries.