You may receive a warning message in the extension about shell initialization conflicts when opening a built-in terminal with the nRF Connect profile. This warning appears when the built-in terminal sets the shell environment to the toolchain and SDK versions it is supposed to use, but the shell initialization script (for example, .bashrc) overrides the environment. This can happen if the ZEPHYR_BASE environment variable is set in .bashrc.
To fix this issue, if there is no need for external terminals to use the ZEPHYR_BASE variable, you can remove this variable from .bashrc. Alternatively, you can move it to .bash_profile or an equivalent script that is only loaded by login shells.