This can sometimes happen when changing themes – different themes use different widget IDs, and if they somehow use the same ones, those widgets can change places.
The good news is that they should all be accessible if you go to “Appearance > Widgets” – all of your widgets are drag and droppable, so you might just want to take note (or leave a tab open) using your old theme so you can see which widgets go where, and then rearrange them once GP is activated.