I also lost all stats when I switched over to the JetPack version of WordPress Stats. I did this on my personal site, which is a “sandbox” for trying new ideas, but before migrating our other sites to JetPack (where our stats canNOT just disappear), I would need to know that this issue is resolved.
I also noticed that when I deactivated and reactivated Stats (while moving to WordPress MultiSite), the stats were *again* reset to zero.