You can list breakpoints with:
info break
This will list all breakpoints. Then a breakpoint can be deleted by its corresponding number:
del 3
For example:
(gdb) info b
Num Type Disp Enb Address What
3 breakpoint keep y 0x004018c3 in timeCorrect at my3.c:215
4 breakpoint keep y 0x004295b0 in avi_write_packet atlibavformat/avienc.c:513
(gdb) del 3
(gdb) info b
Num Type Disp Enb Address What
4 breakpoint keep y 0x004295b0 in avi_write_packet atlibavformat/avienc.c:513
Try these (reference):
clear linenum
clear filename:linenum