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matt6575 commented
Does the out node run before anything else in the flow? Is there a way to insure for example data gets put back into a graph before any other data is added?
I have also run into an issue where I lose my data after a NR upgrade. I have no issue with data being retained during a deploy, restarting flows, restarting NR, or restarting the computer it is running on. But each time I upgrade NR to the latest version my data seems to disappear. Looking at the json files confirms the data is gone. If I then try and restore the json files from a system image that was taken prior to the NR update and force the out node to run, that json file is over-written with a new empty file.