[Python] How to fix “WARNING: overwriting environment variables set in the machine overwriting...

When I activate my Python environment it says

WARNING: overwriting environment variables set in the machine overwriting variable [‘PATH’].


I also noticed because of this most of the commands I use within the environment including jupyter notebook don’t work. This problem started when I made a mistake while integrating another software which I now successfully have integrated.

To reproduce it I open up Anaconda Prompt then within the terminal I activate my environment with conda activate bash1pilot. When it’s activated I can tell there is a problem not just because of the warning message but also because the commands thereafter don’t work properly such as jupyter notebook which is the program I’m trying to access.

When it's working it's supposed to direct me to Jupyter-Notebook when I do the command but when I run jupyter notebook, it doesn't work because of the error.

In addition to this, it was working perfectly until I was trying to integrate a different program but I made a mistake during the integration process which likely led me to this problem. If I had to guess it could be a directory issue. If I were to retrace my steps this is what I remember doing:

conda activate bash1pilot
set PATH=%PATH%;C:\Users\User\Desktop\gmsh-4.11.1-Windows64


then I closed and reopened Anaconda

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