Notes2.db-journal is temporary file that database engine creates while updating main database. It should be automatically deleted. It's seems as some file system error occurred while Flashnote trying to save its database.
It is working good now, but my faith has shaken a bit. It has become so important and I had so many tidbits it that, what if it disappears.
About backup, I suggest you use any backup utility to automatic flashnote database. Or you can do this by hand using File -> Export databases to txt files.
hmm. we need something within flashnote to do it. There is no point in taking the backup of entire hd for just this file.
And, the export database is not at all practical as it creates a folder for every note and puts subnotes in individual separate files. So if we need to check something, we need to open each file one by one. Not practical. It would help if it given option to save entire database to a single text file.
I don't know now how Flashnote will develop further. Probably I will rewrite it from scratch. I am trying to do this now, but I am very busy with other projects, so I can not promise.
Having been using pc for 25 years, having pc/ net at my home for last 10 years, and having used 1000s of softwares, I can say that Flashnote is an outright winner utility. It is so simple, so convenient, so useful. With proper advertising, I am sure that every user would install it on his pc.
so, don't give up on this utility. Your concept is an essential basic for every pc. It needs some improvements that will increase its convenience multifold, but it is very useful without that itself.