Hi Wesley,
When you unplug your PS4, do you shut it down as it should (power off option instead stand by mode). You always should turn it off completely before you unplug it.
Testing:
* Turn it off completely, unplug it, does it still need to “check the system storage” ?
* When you put it in Stand by mode, does everything works good or is still telling you to check the storage?
* Is it possible to test with another harddrive (perhaps to test with a harddrive from an old laptop)?