I checked the console I was getting errors like this:
This graph has a nodeview with id:03890bcc-a32c-46d1-9812-3e34adbdcb4c and name:String, but does not contain a matching nodeModel
This appears to be the same issue as this tread: Nodes and Wires Missing When Opening DYN File
After removing all addins and installing them back one at a time, I can confirm the error is caused by PyRevit. I will follow up with them to resolve this.