First a bit about syncing. You have one primary computer, the one you first set up syncing on using MONEYDANCE – SYNCING and any number of secondary computers set up using MONEYDANCE – NEW – OPEN SYNCED FILE. You can change the sync method on your primary computer but not on a secondary computer.
However, if you restore your primary computer from a secondary computer backup your syncing method will be greyed out and you will not be able to change it. Make sure the auto backups for the primary and secondary computers are not set to use the same location if you are say using Dropbox.
It is possible to convert a secondary data set to a primary data set if you find all your computers have a secondary data set.
If you think this the case I can post a script to convert a secondary data set to a primary data set.