I have exactly the same problem as SoheylV and LeBobbyshoot from the last couple days.
LabVIEW RT 2017 f2 running on cRIO-9067. Every time I open the project the same 5 of my 162 shared variables in saved in 2 of 4 lvlibs complain they are not in the project. This application was migrated from an working system running LV 2014 and the problem occurred on this machine in LV 2014 also.
1. Using the Select Variable... menu the variable is visible but cannot be selected
2. Show Variable in Project is greyed out
3. Dragging the same variable from the project to the VI shows a broken variable (black)
4. Deleting the variable and recreating it in another lvlib and it is broken on the next open
5.Find Callers from the variable in the project shows all the same broken VIs as having the variable!!!
The problem is the same regardless of the cRIO being connected or the variables being deployed. All the variables are hosted on the cRIO. One variable is a simple array of Booleans. Another computer shows the exact same results. Attached is the software installed on the cRIO.