The chance of that happening is roughly equal to the chance of a collision randomly occurring somewhere in a few quadrillion SHA256 hashes.
https://crypto.stackexchange.com/questions/52261/birthday-at...
http://www.npr.org/sections/krulwich/2012/09/17/161096233/wh...
https://www.cnet.com/news/the-milky-way-is-flush-with-habita...
Hash functions tend to be broken gradually and publicly, and we migrate to new ones as they start to look shaky. It's theoretically possible for someone to privately break a function that everyone else thinks is secure, but it would be an extremely impressive achievement since lots of full-time cryptographers work on breaking these things and publish every little bit of progress they make.
Also, it's highly likely that flaws will be found with the hash algorithm long before 12 million years are up.
Obviously we wouldn't use the same hash algorithm and setup for 12 million years, but the sheer absurdity of that length of time and that pace of content production shows this method will last, at least until flaws are found in SHA256.
I think even 0.01% would be enough to harm usability.