Yes, it’s done like that. Seach for “redirectors” term on Unreal sites.
There are created automatically and I have habits of using “Fix redirectors” every time I perform a cleanup.
The problem could appear if you moved a map file like any other file. In game engines is usually better to open map and use “Save as” to move map to new location. Fix references to your map in your project (if needed) and remove old file.
And yes, working without source control on game/code project is risky. Too many files, dependencies, references 
Never move files in Explorer. It doesn’t care about references. It doesn’t care about fact that code class of blueprint is named after file name. It doesn’t care about anything
Although still I don’t know why your files got messed up.