The data is probably not lost. Manager is good about that.
If it has been a while since you last updated, recent changes may have caused Manager to pick up an old copy of your business file. You may need to import the latest version of your business file.
There is a troubleshooting guide here:Lost businesses or recent data after upgrading
Thanks @Abeiku
And try reading through this post: Added budgeting (+ going back to Application Data folder).