Hi Sean,
Deleting the sync file and any data in the mSecure folder in your Dropbox account will not harm the data stored in the mSecure app. However, if you are still using Dropbox syncing, that data will just be recreated. If all you use Dropbox for is mSecure, I would actually suggest deleting other information so you are sure mSecure has enough space to sync your data.
Sean
My Dropbox is full and the only thing I use it for is to back up/sync mSecure. Does anyone know if it’s ok to delete the old sync files from years past?