How do I remove a single breakpoint with GDB?

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