Just had this problem; run my server external to Eclipse, and use a debug connection.
Breakpoint set, but when stops, Eclipse complains can’t find source.
Clicking the ‘edit Source path’ button, I could see the source folders there. Eclipse would flash the source code, and then very quickly go to the ‘source not found…’.
Finally modified the paths. Rather than using explicit folders, I removed all the folders, and did add project… This appears to be what Eclipse requires.
Documenting for others that have run into it, and for myself the next time I experience it, and have forgotten what I did to fix it…