I had same problem, but it was solved.
1. Delete all the folders and files in three folder: config-store, directories and logs
2. Run Configure ArcGIS Server Account (in program files shortcut) to reconfigure the account
Done
I encountered the same issue in ArcGIS Server 10.6 ... updating directories location from one network path(A) to another(B),
Updating directories location for arcgisconfig, arcgiscache & arcgisoutput, worked well, without any errors
.
However, while updating/changing location for arcgisjobs & arcgissystem directories, i faced this issue
Below steps helped me to resolve it:
1. Updated folder location of arcgisjobs and arcgissystem to c:/temp/arcgisjobs and c:/temp/arcgissystem
2. Updated folder location of above dir's to desired network location path(B) (Faced same issue)
2. Updated folder location of above dir's to different Network location (C)
4. Updated folder location of above dir's to desired network location path(B)
I hope this will help