WP Toolkit Smart Update .htaccess error

Operating System & Version
CentOS 7.9
cPanel & WHM Version


Jul 19, 2021
cPanel Access Level
Root Administrator
I just got started with WP Toolkit Deluxe, and I'm getting the following error most times I attempt to run Smart Update on the three websites I've tried so far:

Unable to perform Smart Update on this website. Smart Update has detected that your .htaccess file is customized in a way that could prevent the creation of a properly functioning website clone. Please check and adjust .htaccess file customizations, then try running Smart Update again.
This is happening on original sites and staging clones. The error is inconsistent, for example on one website:
  1. Got the error when running Smart Update on the original copy of the site
  2. Cloned to a staging copy, ran Smart Update again, and got the error
  3. Checked the .htaccess file on the staging site, saw that the only thing in there was a small cPanel generated section (the original .htaccess file was not cloned), and copied in the standard WordPress block from the live site. No error that time
  4. Had more updates to install after the successful run and got the error again without touching the .htaccess file or making any other changes to the site whatsoever beyond the successful Smart Update

So the error will occur with any of the following .htaccess scenarios:
  1. cPanel-generated section + WordPress-generated section + W3 Total Cache-generated section
  2. cPanel-generated section + WordPress-generated section
  3. cPanel-generated section alone

And yet sometimes it works fine. I can't make sense of it, so I assume there's something else going on unrelated to the .htaccess files, but somehow that's the error that's being displayed rather than a more appropriate one.

Is there a debugging option or a detailed log or something?