There are 2 issues here:
1) the lps contains settings for a none existing file. That should probably be fixed. Though it may depend on how the file was deleted, and if the IDE was aware of it been deleted.
2) The breakpoint is actually set, in a "different" file. "different" here meaning a file in a different folder, but with the same name.
This can currently not be fixed. If the IDE tries to set a breakpoint using full path info, then in certain cases gdb will not set it, even though the file exists. Therefore breakpoints are handed to gdb by filename only.
So if the file exists by name, even in a different path, then the breakpoint will be set.