a tiny hint: If you work with the SE80 and you set an external breakpoint (BP) it is stored in the tables ABDBG_BPS, ABDBG_EXTDBPS and a few information in the table ABDBG_INFO. As far as I can see, if you work with ABAP in Eclipse (AiE) the content of this tables has no influence.
But if you set the debug properties to a specific user like this
you can find the information in the table ABDBG_EXTDBPS, but without influence to the SE80.
If you set a line BP in AiE a few information are stored in the file .metadata/.plugins/org.eclipse.core.resources/.projects/[SID]_[Client]_[User]_[Language]/.markers or .markers.snap.