If you changed the categories/sub menus of some plugins with PiCo, you either have to use the same feature to change them back to the old category names or you have to delete and reinstall the plugins again. Alternatively if you made a backup of the plugins before changing their categories, you can use it to restore the plugin categories. PiCo itself does not do an automated backup.
No sure why new plugins do not show up in PiCo. There could be many different reasons.
Plugin Commander Listing Reset?
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