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Stepp,
I am far from an expert in either EnergyPlus or BEopt, but I did take a stab at trying to compare internal BEopt results with an identical* EnergyPlus-native IDF. You may already know that BEopt v2.0 generates E+ v8.0 IDFs. I found that these will run in E+ v8.0 with no problems. BEopt v2.8 generates E+ v8.8 IDFs. There appears to be considerably more pre-processing and a more customized implementation of the E+ engine. The BEopt-generated v8.8 IDFs would not run in E+ v8.8 for me. Your upconversion to E+ v9.x likely carried that incompatibility forward. Depending on your objective, you might make your base model in BEopt v2.0 and convert the v8.0 IDF to the current E+ version. From my experience, the geometry, assemblies, equipment, and BEopt defaults would carry forward and have basic functionality.
I realize this solution requires you to repeat some work, and you should test with a basic model to see if you get acceptable results, but it might be a workaround until someone with more knowledge can weigh in. Good luck!
-Ben
*My investigations were comparing the PNNL single-family prototype model to an equally-specified BEopt model in both v2.0/8.0 and v2.8/8.8. We found dramatically different end uses and performance trends, even attempting to change/align with NREL's default schedules and equipment assumptions. Check other posts here to get a better understanding of the challenges when converting HVAC systems into or out of E+; it isn't straightforward.