I have done this with both a Sprint Note 2 and Note 3 and found I had the same problem with both phones. After I used CDMA Tools to write the NV Items, NAM 1&2, then use DFS to put in the profile info and change the MEID I reboot the phone and am no longer able to connect to the phone in either program until I do a factory reset on the phone. After rebooting I verify that the ##3424# settings are correct and put the phone in debugging mode again (because it usually turns off after reboot) but I am not able to connect to the phone, unless I do a factory reset, even if I reboot the computer.
I have been able to succesfully flash both phones to Boost and have everything working, so that is not my problem , but it is time consuming for me since I can only connect to the phone once and input all the info in without resseting the phone (since im not an expert and may need to connect more than once with DFS or CDMA tools). Is this normal when flashing?