While I also do not know how or why a second folder was created, one might add that the sole purpose of the DONOTDELETE.txt file AFAIK is to stop certain android versions from deleting empty folders, which the .stfolder usually is.
So it is safe to remove it, but if you notice syncthing stopped working at some point, chances are that your android has an even stronger urge to keep the filesystem “clean” than you. 