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The integration between Wolfram Workbench (Core 1.0.0.7) and Mathematica 13.1 is partly gammy (as of latest versions 2022-08-23)
Dr Darren: As WORKAROUND I’m currently just using << (a.k.a. Get) to reload specific packages or groups of them as I need in the Notebook, then run CLI input line commands in the Notebook (I side-step the syncing), works fine.