I had the same problem.
‘Periodic workspace save.’ has encountered a problem.
Could not write metadata for ‘/External Files’. D:\java\fuentes\.metadata\.plugins\org.eclipse.core.resources\.projects\External
Files\.markers.snap (El sistema no puede hallar la ruta especificada)
I created the folder “External Files” and it worked fine. In a few minutes the files “.markers.snap” and “.syncinfo.snap” appeared in this folder and the message didn´t appear any more.