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Hi Halcyon_Digest,
Unfortunately, we had to break preset compatibility going from V2.3 to V3.0. We needed a new preset format to encapsulate these new features that so many of our users requested (preset naming, output volume). So, yes, you'll have use catchup mode and write down all your presets. Deeply sorry for the inconvenience.
Of course, you don't have to do this with any factory presets, just initialize after updating and those will be fine. Also, I would recommend getting the latest version of FactorLib from the PF support page.
I also recommend v3.5 for PF, it fixes a number of bugs from v3.0 and has MIDICLK enhancements.