The fact that you didn’t switch the sync target, but set it for the first time and still lost data, leaves me rather concerned. This should not happen. Someone just opened an issue on github:
We will have to wait for @laurent to comment on this problem.
The only way I can think of to get your notes back is to use one of those undelete programs for Windows. Deleted notes are not moved to the trash. There are just unlinked from the filesystem.