So this all started when one of the production servers started to behave oddly. It would start up work for a while then crash with something like this:
InnoDB: Tried to read 16384 bytes at offset 0. Was only able to read 0. InnoDB: Operating system error number 2 in a file operation. InnoDB: The error means the system cannot find the path specified. InnoDB: If you are installing InnoDB, remember that you must create InnoDB: directories yourself, InnoDB does not create them.