I like the fact we get a message if a file changes but it would be good if we could dismiss the message rather then wait the (60?) days for it to disappear if we know about the file change and its ok. Sorry not sure how many days it takes for the message to go or if we can dismiss.
There should be not health check warnings unless you have patched files which should be avoided if possible.
If not possible, you could always just updated hashes.json with the correct hash to make the message disappear.