To make it easier to see which Manager business you are working on you can Rename Businesses to something like “MyBusiness - cloud” or “MyBusiness - Local” (of course if you back up and restore to another location you would have to change the name again.
After you have all your data in one place you may want to minimise the chance of it happening again. You can do that by backing up your data (again) then Removing the Business from the location you are not currently using or