unable to toggle breakpoint eclipse marker id not found

As a workaround, just close the specific java file in Eclipse editor and open it again.

This has been reported here at bugs.eclipse.org.

The report says the affected version is 4.7.1a. The status of the bug is RESOLVED FIXED in v4.8, so we still encounter this issue with the version 4.7.3a (which is the current while writing).

As a workaround, you can close and reopen the GUI, this makes things normal again.