manual nf-core pipelines sync deletes my pixi environment

Description of the bug

I'm attempting to do a manual nf-core pipelines sync to the latest template, however I installed nf-core, and nextflow in a pixi environment.
Part of the command apparently deletes everything on the TEMPLATE branch, which includes my pixi files and pixi environment.

Command used and terminal output

% pixi init -c conda-forge -c bioconda -p linux-64 -p osx-arm64
% pixi add nextflow nf-core nf-test
% pixi shell
% nf-core pipelines sync


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.2.0 - https://nf-co.re


WARNING  Could not find GitHub authentication token. Some API requests may fail.                
INFO     Pipeline directory: /Users/mahpa906/Documents/Projects/nf-core-ameta                   
INFO     Original pipeline repository branch is 'dev'                                           
INFO     Deleting all files in 'TEMPLATE' branch                                                
INFO     Making a new template pipeline using pipeline variables                                
ERROR    Failed to rebuild pipeline from template with error:                                   
         It looks like nextflow is not installed. Please ensure it is available in your PATH.

System information

No response

Reproduce the reported nf-core pipelines sync flow with a pixi environment and inspect the sync command's template-branch cleanup and pipeline rebuild steps. Check how the command discovers nextflow in the active environment and how failures are handled after deletion; done means the sync no longer destroys user files and reports or handles the environment issue safely.