Plugins have disappeared

I seem to have lost all my plugins – not sure when. I went to upload a new logo, and it was then that i realised Jetpack was missing.
On my plugin part of dashboard it says I have no plugins – yet when I try to reinstall the ones I need it tells me that its not possible because the folders are already there.
Has a theme update caused this? How do I resolve this?
thanks, Tara