Stomps Presets Disappeared?

If you go into Rig Manager they should be in the presets folder so you should be able to transfer them back to the KPA presets folder in RM and have them sync. I think they disappeared because of the way the latest OS handles Rigs and Presets independently.

Assuming that you have used these presets in Rigs. You could simply open the effect modules based on these presets and create new presets. You might want to change the preset names anyhow as on the new effect selection screen effect presets are already organized by effect category and type.