Lost AT+ commands on ESP8266 after flashing with "blink" sketch
Thank you Juraj! 

I had attempted to update the firmware multiple times and after 6hrs of trying was giving up. I really thought I had trashed my ESP-01. My post here was my last attempt to resolve the issue. I tend to have a problem of not asking for help until I'm frustrated. I saw your comment, and even though I had already attempted to reflash with new firmware I realized that you knew something I did not, and hopefully I could still salvage the ESP-01. So I downloaded documents about the esp8266 and decided to give it another try. What I found is my ignorance had let me believe that the esp-01 was broken when it was functioning as it should. Anytime you upload new firmware it will replace the old (including the at commands, but that's what it suppose to do). I then found this page that brought to my attention the mistake I was making. I was flashing the files to the wrong address, and there are multiple locations where the "blank" file needs to be flashed to.     So all is back to normal. At commands have returned. Now I have to remove them again to upload my program :).    

https://www.allaboutcircuits.com/projects/flashing-the-ESP-01-firmware-to-SDK-v2.0.0-is-easier-now

I almost forgot to mention, I also had to hard wire my GPIO0 pin to ground before flashing. I was originally pulling GPIO0 to ground with a button. However, even though the serial console showed that I had booted in flash mode the flash tool failed. Only after hardwiring the GPIO0 to ground would the flash tool work.