This is definitely a cool idea, but there could be potential issues if it is to be relied upon for long periods of time. If at any point in the future the hash algorithm used (SHA256 right now it seems) is found to be vulnerable then it could invalidate all past certifications. You don't really even need a full collision attack, a chosen prefix collision attack is enough to completely destroy the system's validity. MD5 is already vulnerable to chosen prefix attacks, maybe in 5 or 10 years SHA256 will be too...

Perhaps using a combination of different hash algorithms that we know are secure today to certify a file together would be a potential solution to the problem. It's not perfect, but at least this way all the algorithms used need to be compromised for the certification to break.