The ColdFusion 2021 server auto-lockdown tool 'Sets file system permissions for your web root'. Is there an option to skip this step? This size of our webroot is huge

That's pretty much the baseline of web app security. You do not want to skip that step.

I have already set the file permissions on the webroot

'Sets file system permissions for your web root'. Is there an option to skip this step?

I have already set the file permissions on the webroot

Those two statements seem to contradict each other, so I dunno what yer actually asking in that case.

The auto lockdown tool sets file permissions on the webroot and I would like to optionally skip this step. I am hoping there is a command line flag that is available. The reason I would like to do this is because the lockdown tool seems to make a backup of the ACL for every single file in the webroot. This takes a very long time, and I have already set the correct file permissions.

the lockdown tool seems to make a backup of the ACL for every single file

EEEEEEEEK. Yeah, fair enough. Sorry, overlooked the "auto" in yer initial Q.