When using Scan Engine and FPGA modes at the same time the compiler has to combine the default RIO Scan Interface bitfile as well as the user FPGA code that was created into one bitfile. Doing this essentially means that the scan engine is running in your bitfile.
This means that to use an I/O variable, you must ensure the FPGA code is running first. If you try to access an I/O variable before you have opened a reference to the FPGA VI or after you have closed a reference to the FPGA VI, then you will get this error.
Alternatively, if you are getting Error -65589 after correcting Error -65536, please make sure that the FIFOs are initializing completely before executing the Scan Engine calls.
It is also possible to receive this error in initial calls to the IO variable or UDV after opening the FPGA reference.