burn arduino bootloader and compiled sketch at same time How can I write the bootloader and sketch code to an Arduino through the ISP and then write the sketch code again using the Arduino IDE later?

Currently, I can write the bootloader through the ISP and then write the sketch through the Arduino IDE.  This works just like normal.

I can also write the bootloader and sketch through the ISP.  The code runs like normal, but I can't load a new version of the sketch through the Arduino IDE.  It just timesout.

Here's what the IDE says when it attempts to upload the program:

avrdude: Version 6.0.1, compiled on Apr 15 2015 at 19:59:58
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "C:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf"

         Using Port                    : COM5
         Using Programmer              : wiring
         Overriding Baud Rate          : 115200
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_getsync(): timeout communicating with programmer


The Arduino IDE creates two hex files after compiling the sketch: one is just the compiled sketch (Sketch.ino.hex) and the other is the compiled sketch with the bootloader code appended to the end (Sketch.ino.with_bootloader.hex).  So, I feel like this should be possible because Arduino produces the file for me.
If you program via ISP, it erases the boot loader, because you do not need it. The whole point of the boot loader is to allow programming over USB. So if you want to use the normal Arduino USB input to program, burn the bootloader and then do not use the ISP.

Note my knowledge of this dates back to older arduino ~1.0 software, it is possible modifications have been made, but the above should still be true. If you have an ISP you do not need the bootloader at all.