All,
If you are experiencing this same issue I am afraid to tell you this, but it appears the only option you have is to reformat your drive and do a clean install of whatever operating system you have installed on your MacBook. For me, this all started when I was having issues with Boot Camp Assistant, I ran Boot Camp Assistant to remove the Windows partition from my MacBook and it gave me an error, so I ended up reformatting my drive, and partitioning the drive manually instead of doing so through Boot Camp Assistant. This seemed to work, but I noticed when I logged into my Mac side, the Windows partition was not visible, it didn't acknowledge the drive, in addition I noticed times when certain folders on my Macintosh HD just were not accessible. I think the only way to resolve this issue is to do a back up, reformat or erase all contents on your Macintosh HD, and start fresh. It may not have anything to do with Boot Camp or Boot Camp Assistant, but this is just one of the things I noticed with my process that may be similar to your situation. Another factor I think can be Apple File System, which comes with Mac OS High Sierra, when I did a clean install I reformatted my drive entirely, and reinstalled from Mac OS X Lion, and then upgraded to High Sierra. I think this could have potentially caused issues as well, so to be safe I would just do a clean install of High Sierra if your Mac is capable of running that and it should work fine. Just be sure to back up all your files before reformatting your Macintosh HD. Good luck!