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Can you please let me know the exact steps to reproduce this issue?
I was able to observe this only when there was already a debug session running. Please check the Debug tab for any stale sessions and clear them as shown below:
When the error occurs can you check how the KitProg3 is enumerating in the device manager? Please provide a screenshot of the same.
Also, let us know which OS you are using.
I have experienced similar situation with gdb when it fails to attach or connect to the target,
although the tool was not ModusToolbox. (I think that it was ARM DS-5)
At that time, all I needed was to terminate the remaining gdb related tasks from Windows Task Manager.
I don't know if this works for MTB, but I hope that it's worth trying.
BTW, about the title of the question, may be off the point though,
I could find gdb in <MTB Install Folder>\tools_2.1\gcc-7.2.1\bin\arm-none-eabi-gdb.exe
And starting it from the "command prompt" showed me the version.