"._" Files causing spontaneous folder invisibility?

I'm managing a school administrator's MacBook Pro 2012 running El Capitan 10.11.6 and have encountered a baffling issue where some of the person's folders seem to be going invisible all on their own with no apparent cause. Spotlight could still find the folders and display their contents and they were readily found and browsed using the ls command in Terminal.


Process

I performed some of the usual diagnostic routines to resolve Finder items not showing up correctly including:

1. Relaunching Finder

2. Restarting computer

3. Resetting PRAM

In addition, I ran some tasks using third party diagnostic tools to try and clear up any display or directory issues that may be at play:

1. Rebuilt display of folders' contents using Onyx by Titanium Software

2. Rebuilt partition directory using Disk Warrior by Alsoft

Discovery

After these tasks turned up no solutions to the issue, I returned to Terminal and started looking for extended attributes and flags. What found was a bevy of invisible files that bore the names of these hidden directories, prefixed by a "._"


I used the cp command to make a copy of the whole directory onto an SD card to explore further and found that when I removed the ._ file, the folder reappeared in Finder and began behaving predictably.


Question

This brings me to the present. I understand that these ._ files are metadata files of sorts and that they may contain critical information to the proper functioning of files and folders. Where I'm stuck is why these directories began gathering ._ files to begin with and whether my solution of deleting them is going to land me and this admin in a pile of trouble in the coming weeks. Is there something here that I'm missing or have I misdiagnosed this issue? What can I do to restore the visibility of these user folders and prevent them from going invisible again?


Any illumination would be greatly appreciated!

Chris